Starting phenix.real_space_refine on Sat Jun 14 11:03:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8u73_41967/06_2025/8u73_41967_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8u73_41967/06_2025/8u73_41967.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8u73_41967/06_2025/8u73_41967.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8u73_41967/06_2025/8u73_41967.map" model { file = "/net/cci-nas-00/data/ceres_data/8u73_41967/06_2025/8u73_41967_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8u73_41967/06_2025/8u73_41967_neut.cif" } resolution = 3.1 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= 0.006 sd= 0.066 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 1 5.49 5 S 84 5.16 5 C 10632 2.51 5 N 2616 2.21 5 O 2866 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 16199 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 7912 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1003, 7912 Classifications: {'peptide': 1003} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 972} Chain breaks: 5 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 7912 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1003, 7912 Classifications: {'peptide': 1003} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 972} Chain breaks: 5 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 217 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 217 Unusual residues: {'AJP': 2, 'POV': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 104 Unresolved non-hydrogen chiralities: 18 Chain: "B" Number of atoms: 158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 158 Unusual residues: {'AJP': 2, 'POV': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 103 Unresolved non-hydrogen dihedrals: 130 Unresolved non-hydrogen chiralities: 23 Time building chain proxies: 9.62, per 1000 atoms: 0.59 Number of scatterers: 16199 At special positions: 0 Unit cell: (106.76, 132.6, 125.12, 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 84 16.00 P 1 15.00 O 2866 8.00 N 2616 7.00 C 10632 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.64 Conformation dependent library (CDL) restraints added in 1.8 seconds 3964 Ramachandran restraints generated. 1982 Oldfield, 0 Emsley, 1982 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3780 Finding SS restraints... Secondary structure from input PDB file: 87 helices and 9 sheets defined 73.6% alpha, 4.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.59 Creating SS restraints... Processing helix chain 'A' and resid 77 through 95 Processing helix chain 'A' and resid 102 through 120 Processing helix chain 'A' and resid 120 through 132 removed outlier: 4.750A pdb=" N ASP A 129 " --> pdb=" O GLU A 125 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N VAL A 130 " --> pdb=" O HIS A 126 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N HIS A 132 " --> pdb=" O ARG A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 141 removed outlier: 3.876A pdb=" N LEU A 138 " --> pdb=" O ASP A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 154 removed outlier: 3.720A pdb=" N SER A 150 " --> pdb=" O LEU A 146 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N MET A 154 " --> pdb=" O SER A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 161 No H-bonds generated for 'chain 'A' and resid 159 through 161' Processing helix chain 'A' and resid 162 through 188 Processing helix chain 'A' and resid 194 through 205 Processing helix chain 'A' and resid 210 through 219 removed outlier: 3.838A pdb=" N ASP A 219 " --> pdb=" O ALA A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 254 removed outlier: 3.651A pdb=" N MET A 251 " --> pdb=" O VAL A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 273 Processing helix chain 'A' and resid 273 through 291 Processing helix chain 'A' and resid 296 through 320 removed outlier: 3.533A pdb=" N GLU A 300 " --> pdb=" O ASP A 296 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N TRP A 318 " --> pdb=" O ILE A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 337 Processing helix chain 'A' and resid 342 through 375 Processing helix chain 'A' and resid 381 through 407 removed outlier: 3.554A pdb=" N TRP A 385 " --> pdb=" O ASP A 381 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N THR A 396 " --> pdb=" O TYR A 392 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ILE A 403 " --> pdb=" O ALA A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 428 removed outlier: 3.604A pdb=" N ALA A 422 " --> pdb=" O THR A 418 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N VAL A 423 " --> pdb=" O TRP A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 447 removed outlier: 3.948A pdb=" N LEU A 436 " --> pdb=" O GLY A 432 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLY A 447 " --> pdb=" O GLU A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 483 removed outlier: 4.376A pdb=" N SER A 453 " --> pdb=" O ASP A 449 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N ALA A 471 " --> pdb=" O LEU A 467 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N GLN A 475 " --> pdb=" O ALA A 471 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N THR A 476 " --> pdb=" O THR A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 486 through 492 removed outlier: 4.204A pdb=" N LYS A 490 " --> pdb=" O ILE A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 514 removed outlier: 3.564A pdb=" N VAL A 498 " --> pdb=" O MET A 494 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N SER A 514 " --> pdb=" O ASN A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 531 removed outlier: 3.770A pdb=" N GLU A 531 " --> pdb=" O THR A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 571 through 600 Processing helix chain 'A' and resid 604 through 621 removed outlier: 3.637A pdb=" N ASP A 620 " --> pdb=" O GLU A 616 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N GLU A 621 " --> pdb=" O VAL A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 632 removed outlier: 3.684A pdb=" N LEU A 631 " --> pdb=" O LEU A 627 " (cutoff:3.500A) Processing helix chain 'A' and resid 633 through 639 removed outlier: 5.263A pdb=" N GLN A 636 " --> pdb=" O LYS A 633 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N ILE A 637 " --> pdb=" O SER A 634 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N LYS A 638 " --> pdb=" O TRP A 635 " (cutoff:3.500A) Processing helix chain 'A' and resid 640 through 653 removed outlier: 4.019A pdb=" N LEU A 644 " --> pdb=" O ILE A 640 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU A 651 " --> pdb=" O LYS A 647 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ILE A 652 " --> pdb=" O LEU A 648 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER A 653 " --> pdb=" O GLU A 649 " (cutoff:3.500A) Processing helix chain 'A' and resid 679 through 697 removed outlier: 4.175A pdb=" N ILE A 684 " --> pdb=" O PHE A 680 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N VAL A 693 " --> pdb=" O VAL A 689 " (cutoff:3.500A) Proline residue: A 694 - end of helix Processing helix chain 'A' and resid 731 through 754 removed outlier: 3.583A pdb=" N SER A 735 " --> pdb=" O ALA A 731 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 761 through 776 removed outlier: 3.626A pdb=" N LYS A 765 " --> pdb=" O SER A 761 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N VAL A 776 " --> pdb=" O VAL A 772 " (cutoff:3.500A) Processing helix chain 'A' and resid 798 through 806 removed outlier: 3.804A pdb=" N LEU A 804 " --> pdb=" O LYS A 800 " (cutoff:3.500A) Processing helix chain 'A' and resid 812 through 854 removed outlier: 3.931A pdb=" N ALA A 816 " --> pdb=" O ARG A 812 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE A 818 " --> pdb=" O THR A 814 " (cutoff:3.500A) Proline residue: A 819 - end of helix removed outlier: 3.822A pdb=" N LEU A 835 " --> pdb=" O ASN A 831 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LYS A 852 " --> pdb=" O GLU A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 855 through 857 No H-bonds generated for 'chain 'A' and resid 855 through 857' Processing helix chain 'A' and resid 860 through 889 removed outlier: 3.963A pdb=" N HIS A 889 " --> pdb=" O LEU A 885 " (cutoff:3.500A) Processing helix chain 'A' and resid 889 through 919 removed outlier: 3.647A pdb=" N ALA A 893 " --> pdb=" O HIS A 889 " (cutoff:3.500A) Processing helix chain 'A' and resid 923 through 942 Processing helix chain 'A' and resid 952 through 959 Processing helix chain 'A' and resid 966 through 976 Processing helix chain 'A' and resid 1043 through 1050 Processing helix chain 'A' and resid 1070 through 1080 Processing helix chain 'A' and resid 1085 through 1107 Proline residue: A1101 - end of helix removed outlier: 3.637A pdb=" N MET A1107 " --> pdb=" O ILE A1103 " (cutoff:3.500A) Processing helix chain 'A' and resid 1113 through 1124 removed outlier: 3.743A pdb=" N ARG A1123 " --> pdb=" O LEU A1119 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLY A1124 " --> pdb=" O HIS A1120 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 95 Processing helix chain 'B' and resid 102 through 120 Processing helix chain 'B' and resid 120 through 132 removed outlier: 4.731A pdb=" N ASP B 129 " --> pdb=" O GLU B 125 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N VAL B 130 " --> pdb=" O HIS B 126 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N HIS B 132 " --> pdb=" O ARG B 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 141 removed outlier: 3.867A pdb=" N LEU B 138 " --> pdb=" O ASP B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 154 removed outlier: 3.716A pdb=" N SER B 150 " --> pdb=" O LEU B 146 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N MET B 154 " --> pdb=" O SER B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 161 No H-bonds generated for 'chain 'B' and resid 159 through 161' Processing helix chain 'B' and resid 162 through 188 Processing helix chain 'B' and resid 194 through 205 Processing helix chain 'B' and resid 210 through 221 removed outlier: 3.886A pdb=" N ASP B 219 " --> pdb=" O ALA B 215 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LEU B 220 " --> pdb=" O LEU B 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 254 removed outlier: 3.650A pdb=" N MET B 251 " --> pdb=" O VAL B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 273 Processing helix chain 'B' and resid 273 through 291 Processing helix chain 'B' and resid 296 through 320 removed outlier: 3.542A pdb=" N GLU B 300 " --> pdb=" O ASP B 296 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N TRP B 318 " --> pdb=" O ILE B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 337 removed outlier: 4.551A pdb=" N VAL B 327 " --> pdb=" O GLY B 323 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASN B 335 " --> pdb=" O GLY B 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 375 Processing helix chain 'B' and resid 381 through 407 removed outlier: 3.555A pdb=" N TRP B 385 " --> pdb=" O ASP B 381 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N THR B 396 " --> pdb=" O TYR B 392 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ILE B 403 " --> pdb=" O ALA B 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 410 through 414 removed outlier: 3.960A pdb=" N ILE B 413 " --> pdb=" O LEU B 410 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLY B 414 " --> pdb=" O SER B 411 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 410 through 414' Processing helix chain 'B' and resid 418 through 428 removed outlier: 3.625A pdb=" N ALA B 422 " --> pdb=" O THR B 418 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N VAL B 423 " --> pdb=" O TRP B 419 " (cutoff:3.500A) Processing helix chain 'B' and resid 432 through 447 removed outlier: 3.885A pdb=" N LEU B 436 " --> pdb=" O GLY B 432 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLY B 447 " --> pdb=" O GLU B 443 " (cutoff:3.500A) Processing helix chain 'B' and resid 449 through 483 removed outlier: 4.374A pdb=" N SER B 453 " --> pdb=" O ASP B 449 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ALA B 471 " --> pdb=" O LEU B 467 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N GLN B 475 " --> pdb=" O ALA B 471 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N THR B 476 " --> pdb=" O THR B 472 " (cutoff:3.500A) Processing helix chain 'B' and resid 486 through 492 removed outlier: 4.211A pdb=" N LYS B 490 " --> pdb=" O ILE B 486 " (cutoff:3.500A) Processing helix chain 'B' and resid 492 through 514 removed outlier: 3.564A pdb=" N VAL B 498 " --> pdb=" O MET B 494 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N SER B 514 " --> pdb=" O ASN B 510 " (cutoff:3.500A) Processing helix chain 'B' and resid 522 through 531 removed outlier: 3.762A pdb=" N GLU B 531 " --> pdb=" O THR B 527 " (cutoff:3.500A) Processing helix chain 'B' and resid 571 through 600 Processing helix chain 'B' and resid 604 through 620 removed outlier: 3.629A pdb=" N ASP B 620 " --> pdb=" O GLU B 616 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 632 removed outlier: 3.687A pdb=" N LEU B 631 " --> pdb=" O LEU B 627 " (cutoff:3.500A) Processing helix chain 'B' and resid 633 through 639 removed outlier: 5.265A pdb=" N GLN B 636 " --> pdb=" O LYS B 633 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N ILE B 637 " --> pdb=" O SER B 634 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N LYS B 638 " --> pdb=" O TRP B 635 " (cutoff:3.500A) Processing helix chain 'B' and resid 640 through 653 removed outlier: 4.004A pdb=" N LEU B 644 " --> pdb=" O ILE B 640 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU B 651 " --> pdb=" O LYS B 647 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ILE B 652 " --> pdb=" O LEU B 648 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SER B 653 " --> pdb=" O GLU B 649 " (cutoff:3.500A) Processing helix chain 'B' and resid 679 through 697 removed outlier: 4.179A pdb=" N ILE B 684 " --> pdb=" O PHE B 680 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N VAL B 693 " --> pdb=" O VAL B 689 " (cutoff:3.500A) Proline residue: B 694 - end of helix Processing helix chain 'B' and resid 731 through 754 removed outlier: 3.577A pdb=" N SER B 735 " --> pdb=" O ALA B 731 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 762 through 776 removed outlier: 3.689A pdb=" N VAL B 776 " --> pdb=" O VAL B 772 " (cutoff:3.500A) Processing helix chain 'B' and resid 798 through 806 removed outlier: 3.799A pdb=" N LEU B 804 " --> pdb=" O LYS B 800 " (cutoff:3.500A) Processing helix chain 'B' and resid 812 through 854 removed outlier: 3.930A pdb=" N ALA B 816 " --> pdb=" O ARG B 812 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ILE B 818 " --> pdb=" O THR B 814 " (cutoff:3.500A) Proline residue: B 819 - end of helix removed outlier: 3.804A pdb=" N LEU B 835 " --> pdb=" O ASN B 831 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LYS B 852 " --> pdb=" O GLU B 848 " (cutoff:3.500A) Processing helix chain 'B' and resid 855 through 857 No H-bonds generated for 'chain 'B' and resid 855 through 857' Processing helix chain 'B' and resid 860 through 889 removed outlier: 3.953A pdb=" N HIS B 889 " --> pdb=" O LEU B 885 " (cutoff:3.500A) Processing helix chain 'B' and resid 889 through 919 removed outlier: 3.635A pdb=" N ALA B 893 " --> pdb=" O HIS B 889 " (cutoff:3.500A) Processing helix chain 'B' and resid 923 through 942 Processing helix chain 'B' and resid 952 through 959 Processing helix chain 'B' and resid 966 through 976 Processing helix chain 'B' and resid 1043 through 1050 Processing helix chain 'B' and resid 1070 through 1080 Processing helix chain 'B' and resid 1085 through 1107 removed outlier: 3.551A pdb=" N VAL B1094 " --> pdb=" O LEU B1090 " (cutoff:3.500A) Proline residue: B1101 - end of helix removed outlier: 3.858A pdb=" N MET B1107 " --> pdb=" O ILE B1103 " (cutoff:3.500A) Processing helix chain 'B' and resid 1113 through 1124 removed outlier: 3.815A pdb=" N ARG B1123 " --> pdb=" O LEU B1119 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLY B1124 " --> pdb=" O HIS B1120 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 977 through 982 removed outlier: 6.280A pdb=" N GLN A1064 " --> pdb=" O VAL A1002 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE A1042 " --> pdb=" O PHE A 999 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 987 through 989 removed outlier: 6.866A pdb=" N VAL A1057 " --> pdb=" O ILE A 988 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1135 through 1136 removed outlier: 4.189A pdb=" N TYR A1153 " --> pdb=" O THR A1175 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1165 through 1166 removed outlier: 3.806A pdb=" N ASP A1144 " --> pdb=" O VAL A1189 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 208 through 209 Processing sheet with id=AA6, first strand: chain 'B' and resid 977 through 982 removed outlier: 6.310A pdb=" N GLN B1064 " --> pdb=" O VAL B1002 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ILE B1042 " --> pdb=" O PHE B 999 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 987 through 989 removed outlier: 6.886A pdb=" N VAL B1057 " --> pdb=" O ILE B 988 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 1135 through 1136 removed outlier: 4.212A pdb=" N TYR B1153 " --> pdb=" O THR B1175 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 1165 through 1166 removed outlier: 3.832A pdb=" N ASP B1144 " --> pdb=" O VAL B1189 " (cutoff:3.500A) 1082 hydrogen bonds defined for protein. 3207 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: 5.05 Time building geometry restraints manager: 4.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2750 1.33 - 1.45: 4053 1.45 - 1.57: 9580 1.57 - 1.70: 2 1.70 - 1.82: 154 Bond restraints: 16539 Sorted by residual: bond pdb=" CA ALA B 497 " pdb=" C ALA B 497 " ideal model delta sigma weight residual 1.523 1.475 0.049 1.30e-02 5.92e+03 1.41e+01 bond pdb=" CA ALA A 497 " pdb=" C ALA A 497 " ideal model delta sigma weight residual 1.523 1.475 0.049 1.30e-02 5.92e+03 1.41e+01 bond pdb=" C TYR A 641 " pdb=" N PRO A 642 " ideal model delta sigma weight residual 1.335 1.381 -0.045 1.36e-02 5.41e+03 1.10e+01 bond pdb=" C TYR B 641 " pdb=" N PRO B 642 " ideal model delta sigma weight residual 1.335 1.380 -0.044 1.36e-02 5.41e+03 1.06e+01 bond pdb=" C ALA A 497 " pdb=" O ALA A 497 " ideal model delta sigma weight residual 1.237 1.206 0.031 1.17e-02 7.31e+03 7.04e+00 ... (remaining 16534 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.44: 22127 2.44 - 4.89: 276 4.89 - 7.33: 50 7.33 - 9.78: 11 9.78 - 12.22: 4 Bond angle restraints: 22468 Sorted by residual: angle pdb=" N GLY A1150 " pdb=" CA GLY A1150 " pdb=" C GLY A1150 " ideal model delta sigma weight residual 112.45 120.84 -8.39 2.10e+00 2.27e-01 1.60e+01 angle pdb=" N GLY B1150 " pdb=" CA GLY B1150 " pdb=" C GLY B1150 " ideal model delta sigma weight residual 112.45 120.49 -8.04 2.10e+00 2.27e-01 1.47e+01 angle pdb=" N TYR A 641 " pdb=" CA TYR A 641 " pdb=" C TYR A 641 " ideal model delta sigma weight residual 109.81 117.74 -7.93 2.21e+00 2.05e-01 1.29e+01 angle pdb=" N TYR B 641 " pdb=" CA TYR B 641 " pdb=" C TYR B 641 " ideal model delta sigma weight residual 109.81 117.68 -7.87 2.21e+00 2.05e-01 1.27e+01 angle pdb=" CA LEU B 651 " pdb=" CB LEU B 651 " pdb=" CG LEU B 651 " ideal model delta sigma weight residual 116.30 128.52 -12.22 3.50e+00 8.16e-02 1.22e+01 ... (remaining 22463 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.56: 9467 25.56 - 51.12: 790 51.12 - 76.68: 91 76.68 - 102.23: 24 102.23 - 127.79: 21 Dihedral angle restraints: 10393 sinusoidal: 4561 harmonic: 5832 Sorted by residual: dihedral pdb=" CA SER B1163 " pdb=" C SER B1163 " pdb=" N PRO B1164 " pdb=" CA PRO B1164 " ideal model delta harmonic sigma weight residual 0.00 -37.36 37.36 0 5.00e+00 4.00e-02 5.58e+01 dihedral pdb=" CA SER A1163 " pdb=" C SER A1163 " pdb=" N PRO A1164 " pdb=" CA PRO A1164 " ideal model delta harmonic sigma weight residual 0.00 -34.95 34.95 0 5.00e+00 4.00e-02 4.88e+01 dihedral pdb=" O31 AJP B1403 " pdb=" C30 AJP B1403 " pdb=" C32 AJP B1403 " pdb=" O33 AJP B1403 " ideal model delta sinusoidal sigma weight residual 177.28 -54.93 -127.79 1 3.00e+01 1.11e-03 1.72e+01 ... (remaining 10390 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 2533 0.077 - 0.154: 191 0.154 - 0.232: 21 0.232 - 0.309: 0 0.309 - 0.386: 1 Chirality restraints: 2746 Sorted by residual: chirality pdb=" CG LEU B 180 " pdb=" CB LEU B 180 " pdb=" CD1 LEU B 180 " pdb=" CD2 LEU B 180 " both_signs ideal model delta sigma weight residual False -2.59 -2.20 -0.39 2.00e-01 2.50e+01 3.72e+00 chirality pdb=" C10 AJP B1403 " pdb=" C08 AJP B1403 " pdb=" C11 AJP B1403 " pdb=" O82 AJP B1403 " both_signs ideal model delta sigma weight residual False 2.61 2.39 0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" C10 AJP A1403 " pdb=" C08 AJP A1403 " pdb=" C11 AJP A1403 " pdb=" O82 AJP A1403 " both_signs ideal model delta sigma weight residual False 2.61 2.39 0.22 2.00e-01 2.50e+01 1.23e+00 ... (remaining 2743 not shown) Planarity restraints: 2701 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 275 " 0.043 5.00e-02 4.00e+02 6.51e-02 6.77e+00 pdb=" N PRO A 276 " -0.113 5.00e-02 4.00e+02 pdb=" CA PRO A 276 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 276 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 275 " -0.042 5.00e-02 4.00e+02 6.39e-02 6.52e+00 pdb=" N PRO B 276 " 0.110 5.00e-02 4.00e+02 pdb=" CA PRO B 276 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO B 276 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP B1112 " -0.013 2.00e-02 2.50e+03 1.33e-02 4.42e+00 pdb=" CG TRP B1112 " 0.035 2.00e-02 2.50e+03 pdb=" CD1 TRP B1112 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 TRP B1112 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP B1112 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP B1112 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP B1112 " -0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP B1112 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP B1112 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP B1112 " -0.004 2.00e-02 2.50e+03 ... (remaining 2698 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 3323 2.78 - 3.31: 15092 3.31 - 3.84: 26474 3.84 - 4.37: 28749 4.37 - 4.90: 52298 Nonbonded interactions: 125936 Sorted by model distance: nonbonded pdb=" O VAL B 123 " pdb=" OG1 THR B 127 " model vdw 2.252 3.040 nonbonded pdb=" CE LYS B 638 " pdb=" CE1 HIS B 889 " model vdw 2.255 3.660 nonbonded pdb=" CE LYS A 638 " pdb=" CE1 HIS A 889 " model vdw 2.256 3.660 nonbonded pdb=" O VAL A 123 " pdb=" OG1 THR A 127 " model vdw 2.259 3.040 nonbonded pdb=" O VAL A 468 " pdb=" OG1 THR A 472 " model vdw 2.290 3.040 ... (remaining 125931 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 74 through 1193 or resid 1401 or (resid 1403 and (name C01 \ or name C02 or name C03 or name C04 or name C05 or name C06 or name C07 or name \ C08 or name C10 or name C11 or name C12 or name C13 or name C14 or name C15 or \ name C16 or name C17 or name C18 or name C19 or name C20 or name C21 or name C22 \ or name C23 or name C24 or name C26 or name C27 or name C28 or name C29 or name \ C30 or name C32 or name C35 or name C36 or name C37 or name C38 or name C39 or \ name C41 or name C55 or name C56 or name C57 or name C58 or name C59 or name C61 \ or name C80 or name C81 or name C83 or name C85 or name O09 or name O25 or name \ O31 or name O33 or name O34 or name O40 or name O42 or name O43 or name O44 or \ name O54 or name O60 or name O63 or name O64 or name O76 or name O77 or name O78 \ or name O79 or name O82 or name O84)))) selection = (chain 'B' and (resid 74 through 1193 or resid 1401 or resid 1403)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.980 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: 0.630 Check model and map are aligned: 0.110 Set scattering table: 0.130 Process input model: 35.240 Find NCS groups from input model: 0.690 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7304 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 16539 Z= 0.221 Angle : 0.717 12.225 22468 Z= 0.370 Chirality : 0.045 0.386 2746 Planarity : 0.005 0.065 2701 Dihedral : 18.620 127.793 6613 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 0.00 % Allowed : 27.01 % Favored : 72.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.45 % 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: 0.84 (0.19), residues: 1982 helix: 1.30 (0.14), residues: 1354 sheet: 0.74 (0.65), residues: 76 loop : -1.30 (0.25), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP B1112 HIS 0.005 0.001 HIS A 889 PHE 0.021 0.001 PHE B 201 TYR 0.013 0.001 TYR A 309 ARG 0.003 0.000 ARG B1169 Details of bonding type rmsd hydrogen bonds : bond 0.11828 ( 1082) hydrogen bonds : angle 5.64412 ( 3207) covalent geometry : bond 0.00378 (16539) covalent geometry : angle 0.71695 (22468) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3964 Ramachandran restraints generated. 1982 Oldfield, 0 Emsley, 1982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3964 Ramachandran restraints generated. 1982 Oldfield, 0 Emsley, 1982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 165 time to evaluate : 1.603 Fit side-chains REVERT: A 1116 LYS cc_start: 0.7641 (tttm) cc_final: 0.7290 (tttm) outliers start: 0 outliers final: 0 residues processed: 165 average time/residue: 0.2523 time to fit residues: 65.1859 Evaluate side-chains 150 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 150 time to evaluate : 1.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 168 optimal weight: 2.9990 chunk 151 optimal weight: 8.9990 chunk 84 optimal weight: 2.9990 chunk 51 optimal weight: 0.5980 chunk 102 optimal weight: 0.0570 chunk 80 optimal weight: 6.9990 chunk 156 optimal weight: 30.0000 chunk 60 optimal weight: 20.0000 chunk 95 optimal weight: 6.9990 chunk 116 optimal weight: 0.7980 chunk 181 optimal weight: 4.9990 overall best weight: 1.4902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.216889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.196865 restraints weight = 17491.380| |-----------------------------------------------------------------------------| r_work (start): 0.4113 rms_B_bonded: 0.98 r_work: 0.3696 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.3434 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.0736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16539 Z= 0.143 Angle : 0.540 8.153 22468 Z= 0.270 Chirality : 0.039 0.209 2746 Planarity : 0.004 0.063 2701 Dihedral : 8.635 108.467 2915 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 3.08 % Allowed : 23.86 % Favored : 73.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.19), residues: 1982 helix: 1.94 (0.14), residues: 1362 sheet: 0.90 (0.63), residues: 76 loop : -1.26 (0.25), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B1112 HIS 0.005 0.001 HIS A 889 PHE 0.016 0.001 PHE B 201 TYR 0.018 0.001 TYR B 309 ARG 0.003 0.000 ARG A 583 Details of bonding type rmsd hydrogen bonds : bond 0.05099 ( 1082) hydrogen bonds : angle 4.23187 ( 3207) covalent geometry : bond 0.00331 (16539) covalent geometry : angle 0.54045 (22468) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3964 Ramachandran restraints generated. 1982 Oldfield, 0 Emsley, 1982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3964 Ramachandran restraints generated. 1982 Oldfield, 0 Emsley, 1982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 161 time to evaluate : 1.593 Fit side-chains REVERT: A 651 LEU cc_start: 0.7078 (OUTLIER) cc_final: 0.6819 (pp) REVERT: A 872 GLU cc_start: 0.7008 (OUTLIER) cc_final: 0.6729 (tp30) REVERT: A 928 HIS cc_start: 0.7594 (m90) cc_final: 0.7388 (m90) REVERT: B 393 LEU cc_start: 0.8819 (OUTLIER) cc_final: 0.8575 (mm) REVERT: B 872 GLU cc_start: 0.7131 (OUTLIER) cc_final: 0.6889 (tp30) outliers start: 53 outliers final: 24 residues processed: 205 average time/residue: 0.2432 time to fit residues: 78.7862 Evaluate side-chains 175 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 147 time to evaluate : 1.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain A residue 844 ILE Chi-restraints excluded: chain A residue 854 ILE Chi-restraints excluded: chain A residue 872 GLU Chi-restraints excluded: chain A residue 989 VAL Chi-restraints excluded: chain A residue 1037 THR Chi-restraints excluded: chain A residue 1047 VAL Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 596 LYS Chi-restraints excluded: chain B residue 844 ILE Chi-restraints excluded: chain B residue 872 GLU Chi-restraints excluded: chain B residue 989 VAL Chi-restraints excluded: chain B residue 1037 THR Chi-restraints excluded: chain B residue 1047 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 84 optimal weight: 0.8980 chunk 52 optimal weight: 3.9990 chunk 58 optimal weight: 9.9990 chunk 137 optimal weight: 0.9980 chunk 33 optimal weight: 9.9990 chunk 176 optimal weight: 0.6980 chunk 65 optimal weight: 0.9990 chunk 189 optimal weight: 2.9990 chunk 157 optimal weight: 0.9980 chunk 175 optimal weight: 0.9980 chunk 90 optimal weight: 4.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1172 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.218310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.197096 restraints weight = 17469.857| |-----------------------------------------------------------------------------| r_work (start): 0.4123 rms_B_bonded: 1.04 r_work: 0.3721 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.3453 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.0886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 16539 Z= 0.110 Angle : 0.479 9.238 22468 Z= 0.245 Chirality : 0.038 0.292 2746 Planarity : 0.004 0.060 2701 Dihedral : 7.681 108.229 2915 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 2.44 % Allowed : 25.38 % Favored : 72.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 1.90 (0.19), residues: 1982 helix: 2.18 (0.14), residues: 1366 sheet: 0.98 (0.62), residues: 76 loop : -1.19 (0.26), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B1112 HIS 0.005 0.001 HIS A 889 PHE 0.015 0.001 PHE B 201 TYR 0.015 0.001 TYR A 309 ARG 0.002 0.000 ARG A 583 Details of bonding type rmsd hydrogen bonds : bond 0.04420 ( 1082) hydrogen bonds : angle 4.02406 ( 3207) covalent geometry : bond 0.00237 (16539) covalent geometry : angle 0.47915 (22468) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3964 Ramachandran restraints generated. 1982 Oldfield, 0 Emsley, 1982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3964 Ramachandran restraints generated. 1982 Oldfield, 0 Emsley, 1982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 156 time to evaluate : 1.666 Fit side-chains REVERT: A 651 LEU cc_start: 0.7120 (OUTLIER) cc_final: 0.6849 (pp) REVERT: A 872 GLU cc_start: 0.6987 (OUTLIER) cc_final: 0.6742 (tp30) REVERT: B 393 LEU cc_start: 0.8811 (OUTLIER) cc_final: 0.8565 (mm) REVERT: B 443 GLU cc_start: 0.8238 (OUTLIER) cc_final: 0.7775 (tm-30) REVERT: B 872 GLU cc_start: 0.7087 (OUTLIER) cc_final: 0.6871 (tp30) outliers start: 42 outliers final: 23 residues processed: 188 average time/residue: 0.2547 time to fit residues: 75.1902 Evaluate side-chains 176 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 148 time to evaluate : 1.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain A residue 316 ASP Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 401 MET Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 640 ILE Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain A residue 872 GLU Chi-restraints excluded: chain A residue 989 VAL Chi-restraints excluded: chain A residue 1037 THR Chi-restraints excluded: chain A residue 1047 VAL Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 443 GLU Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 640 ILE Chi-restraints excluded: chain B residue 872 GLU Chi-restraints excluded: chain B residue 989 VAL Chi-restraints excluded: chain B residue 1037 THR Chi-restraints excluded: chain B residue 1047 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 148 optimal weight: 0.7980 chunk 117 optimal weight: 0.9980 chunk 170 optimal weight: 0.9990 chunk 193 optimal weight: 2.9990 chunk 96 optimal weight: 9.9990 chunk 156 optimal weight: 0.0670 chunk 22 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 153 optimal weight: 2.9990 chunk 127 optimal weight: 0.6980 chunk 122 optimal weight: 2.9990 overall best weight: 0.7118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.220355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.201204 restraints weight = 17505.348| |-----------------------------------------------------------------------------| r_work (start): 0.4149 rms_B_bonded: 0.96 r_work: 0.3782 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.3657 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.1046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 16539 Z= 0.101 Angle : 0.452 7.535 22468 Z= 0.234 Chirality : 0.037 0.167 2746 Planarity : 0.004 0.059 2701 Dihedral : 7.408 108.598 2915 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 2.91 % Allowed : 25.38 % Favored : 71.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 2.11 (0.19), residues: 1982 helix: 2.34 (0.14), residues: 1366 sheet: 1.02 (0.62), residues: 76 loop : -1.10 (0.26), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B1112 HIS 0.004 0.001 HIS B 889 PHE 0.015 0.001 PHE B 201 TYR 0.014 0.001 TYR A 309 ARG 0.001 0.000 ARG A 609 Details of bonding type rmsd hydrogen bonds : bond 0.04067 ( 1082) hydrogen bonds : angle 3.85930 ( 3207) covalent geometry : bond 0.00217 (16539) covalent geometry : angle 0.45161 (22468) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3964 Ramachandran restraints generated. 1982 Oldfield, 0 Emsley, 1982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3964 Ramachandran restraints generated. 1982 Oldfield, 0 Emsley, 1982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 165 time to evaluate : 3.182 Fit side-chains REVERT: A 651 LEU cc_start: 0.6820 (OUTLIER) cc_final: 0.6573 (pp) REVERT: A 872 GLU cc_start: 0.6853 (OUTLIER) cc_final: 0.6623 (tp30) REVERT: B 393 LEU cc_start: 0.8725 (OUTLIER) cc_final: 0.8494 (mm) REVERT: B 443 GLU cc_start: 0.8012 (OUTLIER) cc_final: 0.7560 (tm-30) REVERT: B 872 GLU cc_start: 0.6901 (OUTLIER) cc_final: 0.6686 (tp30) outliers start: 50 outliers final: 30 residues processed: 204 average time/residue: 0.3403 time to fit residues: 111.3729 Evaluate side-chains 186 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 151 time to evaluate : 1.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 401 MET Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 640 ILE Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain A residue 872 GLU Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain A residue 989 VAL Chi-restraints excluded: chain A residue 1037 THR Chi-restraints excluded: chain A residue 1047 VAL Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain B residue 316 ASP Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 401 MET Chi-restraints excluded: chain B residue 443 GLU Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 596 LYS Chi-restraints excluded: chain B residue 640 ILE Chi-restraints excluded: chain B residue 760 VAL Chi-restraints excluded: chain B residue 872 GLU Chi-restraints excluded: chain B residue 941 LEU Chi-restraints excluded: chain B residue 989 VAL Chi-restraints excluded: chain B residue 1037 THR Chi-restraints excluded: chain B residue 1047 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 15 optimal weight: 2.9990 chunk 148 optimal weight: 0.9990 chunk 150 optimal weight: 5.9990 chunk 8 optimal weight: 5.9990 chunk 156 optimal weight: 20.0000 chunk 104 optimal weight: 5.9990 chunk 79 optimal weight: 0.7980 chunk 55 optimal weight: 50.0000 chunk 56 optimal weight: 20.0000 chunk 168 optimal weight: 0.9980 chunk 74 optimal weight: 5.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 877 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.214699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.189671 restraints weight = 17863.554| |-----------------------------------------------------------------------------| r_work (start): 0.4041 rms_B_bonded: 1.11 r_work: 0.3630 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work (final): 0.3630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.1129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 16539 Z= 0.186 Angle : 0.550 7.712 22468 Z= 0.280 Chirality : 0.041 0.318 2746 Planarity : 0.004 0.061 2701 Dihedral : 7.935 107.242 2915 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 4.02 % Allowed : 24.91 % Favored : 71.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.80 (0.19), residues: 1982 helix: 2.12 (0.14), residues: 1364 sheet: 0.14 (0.55), residues: 96 loop : -1.13 (0.27), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B1112 HIS 0.006 0.001 HIS A 889 PHE 0.018 0.001 PHE A 348 TYR 0.017 0.001 TYR B 309 ARG 0.002 0.000 ARG A 500 Details of bonding type rmsd hydrogen bonds : bond 0.05593 ( 1082) hydrogen bonds : angle 4.04888 ( 3207) covalent geometry : bond 0.00456 (16539) covalent geometry : angle 0.54982 (22468) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3964 Ramachandran restraints generated. 1982 Oldfield, 0 Emsley, 1982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3964 Ramachandran restraints generated. 1982 Oldfield, 0 Emsley, 1982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 157 time to evaluate : 1.628 Fit side-chains REVERT: A 188 LEU cc_start: 0.8537 (OUTLIER) cc_final: 0.8295 (tp) REVERT: A 651 LEU cc_start: 0.6931 (OUTLIER) cc_final: 0.6673 (pp) REVERT: A 872 GLU cc_start: 0.6579 (OUTLIER) cc_final: 0.6334 (tp30) REVERT: B 393 LEU cc_start: 0.8803 (OUTLIER) cc_final: 0.8576 (mm) REVERT: B 443 GLU cc_start: 0.7753 (OUTLIER) cc_final: 0.7250 (tm-30) REVERT: B 872 GLU cc_start: 0.6586 (OUTLIER) cc_final: 0.6348 (tp30) outliers start: 69 outliers final: 42 residues processed: 211 average time/residue: 0.2506 time to fit residues: 82.3410 Evaluate side-chains 195 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 147 time to evaluate : 1.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 316 ASP Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 338 LYS Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 401 MET Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 425 MET Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 640 ILE Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain A residue 844 ILE Chi-restraints excluded: chain A residue 854 ILE Chi-restraints excluded: chain A residue 872 GLU Chi-restraints excluded: chain A residue 989 VAL Chi-restraints excluded: chain A residue 1037 THR Chi-restraints excluded: chain A residue 1047 VAL Chi-restraints excluded: chain A residue 1066 TYR Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain B residue 316 ASP Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 401 MET Chi-restraints excluded: chain B residue 424 ILE Chi-restraints excluded: chain B residue 425 MET Chi-restraints excluded: chain B residue 443 GLU Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 640 ILE Chi-restraints excluded: chain B residue 844 ILE Chi-restraints excluded: chain B residue 854 ILE Chi-restraints excluded: chain B residue 872 GLU Chi-restraints excluded: chain B residue 924 GLU Chi-restraints excluded: chain B residue 989 VAL Chi-restraints excluded: chain B residue 1047 VAL Chi-restraints excluded: chain B residue 1143 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 176 optimal weight: 0.8980 chunk 3 optimal weight: 0.5980 chunk 139 optimal weight: 0.7980 chunk 45 optimal weight: 0.6980 chunk 184 optimal weight: 3.9990 chunk 64 optimal weight: 7.9990 chunk 159 optimal weight: 9.9990 chunk 54 optimal weight: 2.9990 chunk 83 optimal weight: 7.9990 chunk 106 optimal weight: 0.8980 chunk 101 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.217844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.192535 restraints weight = 17769.837| |-----------------------------------------------------------------------------| r_work (start): 0.4065 rms_B_bonded: 1.15 r_work: 0.3780 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3726 rms_B_bonded: 2.90 restraints_weight: 0.2500 r_work (final): 0.3726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.1140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 16539 Z= 0.104 Angle : 0.464 7.644 22468 Z= 0.240 Chirality : 0.037 0.195 2746 Planarity : 0.004 0.058 2701 Dihedral : 7.406 104.996 2915 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 2.74 % Allowed : 26.14 % Favored : 71.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 2.13 (0.19), residues: 1982 helix: 2.36 (0.14), residues: 1364 sheet: 0.19 (0.54), residues: 96 loop : -0.97 (0.27), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B1112 HIS 0.004 0.001 HIS A 889 PHE 0.015 0.001 PHE B 201 TYR 0.014 0.001 TYR B 309 ARG 0.001 0.000 ARG A 500 Details of bonding type rmsd hydrogen bonds : bond 0.04261 ( 1082) hydrogen bonds : angle 3.83431 ( 3207) covalent geometry : bond 0.00223 (16539) covalent geometry : angle 0.46387 (22468) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3964 Ramachandran restraints generated. 1982 Oldfield, 0 Emsley, 1982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3964 Ramachandran restraints generated. 1982 Oldfield, 0 Emsley, 1982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 153 time to evaluate : 1.769 Fit side-chains REVERT: A 651 LEU cc_start: 0.6609 (OUTLIER) cc_final: 0.6392 (pp) REVERT: B 393 LEU cc_start: 0.8700 (OUTLIER) cc_final: 0.8477 (mm) REVERT: B 443 GLU cc_start: 0.7845 (OUTLIER) cc_final: 0.7394 (tm-30) REVERT: B 872 GLU cc_start: 0.6692 (OUTLIER) cc_final: 0.6492 (tp30) outliers start: 47 outliers final: 32 residues processed: 189 average time/residue: 0.3631 time to fit residues: 108.7621 Evaluate side-chains 183 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 147 time to evaluate : 2.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain A residue 234 SER Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 316 ASP Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 401 MET Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 596 LYS Chi-restraints excluded: chain A residue 640 ILE Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain A residue 989 VAL Chi-restraints excluded: chain A residue 1037 THR Chi-restraints excluded: chain A residue 1047 VAL Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain B residue 316 ASP Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 342 SER Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 401 MET Chi-restraints excluded: chain B residue 443 GLU Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 640 ILE Chi-restraints excluded: chain B residue 872 GLU Chi-restraints excluded: chain B residue 989 VAL Chi-restraints excluded: chain B residue 1037 THR Chi-restraints excluded: chain B residue 1047 VAL Chi-restraints excluded: chain B residue 1106 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 161 optimal weight: 20.0000 chunk 71 optimal weight: 0.9990 chunk 142 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 137 optimal weight: 1.9990 chunk 160 optimal weight: 0.9990 chunk 78 optimal weight: 7.9990 chunk 53 optimal weight: 0.9990 chunk 152 optimal weight: 0.3980 chunk 145 optimal weight: 3.9990 chunk 157 optimal weight: 9.9990 overall best weight: 1.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.217211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.191886 restraints weight = 17779.066| |-----------------------------------------------------------------------------| r_work (start): 0.4063 rms_B_bonded: 1.12 r_work: 0.3673 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3535 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.1218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16539 Z= 0.115 Angle : 0.481 8.844 22468 Z= 0.246 Chirality : 0.038 0.346 2746 Planarity : 0.004 0.059 2701 Dihedral : 7.296 97.725 2915 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 3.08 % Allowed : 25.73 % Favored : 71.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 2.20 (0.19), residues: 1982 helix: 2.41 (0.14), residues: 1366 sheet: 0.21 (0.54), residues: 96 loop : -0.94 (0.27), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B1112 HIS 0.004 0.001 HIS A 889 PHE 0.016 0.001 PHE B 201 TYR 0.016 0.001 TYR A 309 ARG 0.002 0.000 ARG A 500 Details of bonding type rmsd hydrogen bonds : bond 0.04369 ( 1082) hydrogen bonds : angle 3.82345 ( 3207) covalent geometry : bond 0.00261 (16539) covalent geometry : angle 0.48135 (22468) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3964 Ramachandran restraints generated. 1982 Oldfield, 0 Emsley, 1982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3964 Ramachandran restraints generated. 1982 Oldfield, 0 Emsley, 1982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 152 time to evaluate : 1.921 Fit side-chains REVERT: A 651 LEU cc_start: 0.6978 (OUTLIER) cc_final: 0.6727 (pp) REVERT: B 393 LEU cc_start: 0.8802 (OUTLIER) cc_final: 0.8573 (mm) REVERT: B 443 GLU cc_start: 0.8034 (OUTLIER) cc_final: 0.7576 (tm-30) REVERT: B 525 ILE cc_start: 0.9080 (OUTLIER) cc_final: 0.8879 (mp) REVERT: B 872 GLU cc_start: 0.6930 (OUTLIER) cc_final: 0.6706 (tp30) outliers start: 53 outliers final: 39 residues processed: 194 average time/residue: 0.2919 time to fit residues: 87.8035 Evaluate side-chains 195 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 151 time to evaluate : 1.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 316 ASP Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 401 MET Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 596 LYS Chi-restraints excluded: chain A residue 640 ILE Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain A residue 844 ILE Chi-restraints excluded: chain A residue 872 GLU Chi-restraints excluded: chain A residue 924 GLU Chi-restraints excluded: chain A residue 989 VAL Chi-restraints excluded: chain A residue 1037 THR Chi-restraints excluded: chain A residue 1047 VAL Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain B residue 316 ASP Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 342 SER Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 401 MET Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain B residue 443 GLU Chi-restraints excluded: chain B residue 500 ARG Chi-restraints excluded: chain B residue 525 ILE Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 596 LYS Chi-restraints excluded: chain B residue 640 ILE Chi-restraints excluded: chain B residue 844 ILE Chi-restraints excluded: chain B residue 872 GLU Chi-restraints excluded: chain B residue 941 LEU Chi-restraints excluded: chain B residue 989 VAL Chi-restraints excluded: chain B residue 1037 THR Chi-restraints excluded: chain B residue 1047 VAL Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain B residue 1143 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 61 optimal weight: 20.0000 chunk 141 optimal weight: 0.0870 chunk 73 optimal weight: 3.9990 chunk 83 optimal weight: 5.9990 chunk 28 optimal weight: 1.9990 chunk 113 optimal weight: 5.9990 chunk 198 optimal weight: 0.6980 chunk 179 optimal weight: 0.5980 chunk 49 optimal weight: 2.9990 chunk 100 optimal weight: 0.6980 chunk 178 optimal weight: 2.9990 overall best weight: 0.8160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 832 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.218266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.192641 restraints weight = 17574.872| |-----------------------------------------------------------------------------| r_work (start): 0.4072 rms_B_bonded: 1.13 r_work: 0.3671 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work (final): 0.3671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.1299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 16539 Z= 0.104 Angle : 0.467 7.627 22468 Z= 0.239 Chirality : 0.037 0.299 2746 Planarity : 0.004 0.059 2701 Dihedral : 7.026 82.453 2915 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 3.08 % Allowed : 25.73 % Favored : 71.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 2.25 (0.19), residues: 1982 helix: 2.46 (0.14), residues: 1368 sheet: 0.23 (0.53), residues: 96 loop : -0.99 (0.27), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B1112 HIS 0.003 0.001 HIS A 889 PHE 0.015 0.001 PHE B 201 TYR 0.015 0.001 TYR A 309 ARG 0.002 0.000 ARG A 500 Details of bonding type rmsd hydrogen bonds : bond 0.04079 ( 1082) hydrogen bonds : angle 3.75865 ( 3207) covalent geometry : bond 0.00226 (16539) covalent geometry : angle 0.46738 (22468) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3964 Ramachandran restraints generated. 1982 Oldfield, 0 Emsley, 1982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3964 Ramachandran restraints generated. 1982 Oldfield, 0 Emsley, 1982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 152 time to evaluate : 2.218 Fit side-chains REVERT: A 651 LEU cc_start: 0.6941 (OUTLIER) cc_final: 0.6718 (pp) REVERT: B 393 LEU cc_start: 0.8709 (OUTLIER) cc_final: 0.8453 (mm) REVERT: B 443 GLU cc_start: 0.7724 (OUTLIER) cc_final: 0.7248 (tm-30) REVERT: B 525 ILE cc_start: 0.8998 (OUTLIER) cc_final: 0.8717 (mp) REVERT: B 872 GLU cc_start: 0.6516 (OUTLIER) cc_final: 0.6303 (tp30) outliers start: 53 outliers final: 44 residues processed: 194 average time/residue: 0.3079 time to fit residues: 93.2075 Evaluate side-chains 195 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 146 time to evaluate : 1.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain A residue 234 SER Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 316 ASP Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 401 MET Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 596 LYS Chi-restraints excluded: chain A residue 640 ILE Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain A residue 844 ILE Chi-restraints excluded: chain A residue 872 GLU Chi-restraints excluded: chain A residue 989 VAL Chi-restraints excluded: chain A residue 1037 THR Chi-restraints excluded: chain A residue 1047 VAL Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain B residue 316 ASP Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 342 SER Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 401 MET Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain B residue 443 GLU Chi-restraints excluded: chain B residue 500 ARG Chi-restraints excluded: chain B residue 525 ILE Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 596 LYS Chi-restraints excluded: chain B residue 640 ILE Chi-restraints excluded: chain B residue 844 ILE Chi-restraints excluded: chain B residue 872 GLU Chi-restraints excluded: chain B residue 941 LEU Chi-restraints excluded: chain B residue 989 VAL Chi-restraints excluded: chain B residue 1037 THR Chi-restraints excluded: chain B residue 1047 VAL Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain B residue 1143 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 81 optimal weight: 8.9990 chunk 192 optimal weight: 0.9980 chunk 129 optimal weight: 0.5980 chunk 156 optimal weight: 6.9990 chunk 84 optimal weight: 0.9990 chunk 92 optimal weight: 5.9990 chunk 132 optimal weight: 1.9990 chunk 160 optimal weight: 40.0000 chunk 90 optimal weight: 7.9990 chunk 146 optimal weight: 6.9990 chunk 51 optimal weight: 2.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4403 r_free = 0.4403 target = 0.223083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.191762 restraints weight = 17823.052| |-----------------------------------------------------------------------------| r_work (start): 0.4068 rms_B_bonded: 1.39 r_work: 0.3634 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work (final): 0.3634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.1315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16539 Z= 0.136 Angle : 0.503 7.878 22468 Z= 0.256 Chirality : 0.038 0.282 2746 Planarity : 0.004 0.060 2701 Dihedral : 7.012 78.369 2915 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 3.08 % Allowed : 25.96 % Favored : 70.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 2.15 (0.19), residues: 1982 helix: 2.36 (0.14), residues: 1366 sheet: 0.26 (0.53), residues: 96 loop : -0.97 (0.27), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B1112 HIS 0.004 0.001 HIS A 889 PHE 0.017 0.001 PHE B 201 TYR 0.018 0.001 TYR A 309 ARG 0.002 0.000 ARG A 500 Details of bonding type rmsd hydrogen bonds : bond 0.04742 ( 1082) hydrogen bonds : angle 3.84467 ( 3207) covalent geometry : bond 0.00324 (16539) covalent geometry : angle 0.50335 (22468) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3964 Ramachandran restraints generated. 1982 Oldfield, 0 Emsley, 1982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3964 Ramachandran restraints generated. 1982 Oldfield, 0 Emsley, 1982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 153 time to evaluate : 2.148 Fit side-chains REVERT: A 483 MET cc_start: 0.3049 (ttt) cc_final: 0.2743 (mtm) REVERT: A 651 LEU cc_start: 0.7128 (OUTLIER) cc_final: 0.6894 (pp) REVERT: B 393 LEU cc_start: 0.8791 (OUTLIER) cc_final: 0.8537 (mm) REVERT: B 443 GLU cc_start: 0.7952 (OUTLIER) cc_final: 0.7454 (tm-30) REVERT: B 483 MET cc_start: 0.3097 (ttt) cc_final: 0.2777 (mtm) REVERT: B 506 ASN cc_start: 0.8012 (t0) cc_final: 0.7621 (m-40) REVERT: B 872 GLU cc_start: 0.6635 (OUTLIER) cc_final: 0.6409 (tp30) outliers start: 53 outliers final: 45 residues processed: 196 average time/residue: 0.3647 time to fit residues: 112.7084 Evaluate side-chains 194 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 145 time to evaluate : 3.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain A residue 234 SER Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 316 ASP Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 338 LYS Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 401 MET Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 640 ILE Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain A residue 844 ILE Chi-restraints excluded: chain A residue 872 GLU Chi-restraints excluded: chain A residue 924 GLU Chi-restraints excluded: chain A residue 989 VAL Chi-restraints excluded: chain A residue 1037 THR Chi-restraints excluded: chain A residue 1047 VAL Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain B residue 316 ASP Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 342 SER Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 401 MET Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain B residue 443 GLU Chi-restraints excluded: chain B residue 500 ARG Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 596 LYS Chi-restraints excluded: chain B residue 640 ILE Chi-restraints excluded: chain B residue 844 ILE Chi-restraints excluded: chain B residue 872 GLU Chi-restraints excluded: chain B residue 989 VAL Chi-restraints excluded: chain B residue 1037 THR Chi-restraints excluded: chain B residue 1047 VAL Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain B residue 1143 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 12 optimal weight: 0.6980 chunk 192 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 9 optimal weight: 6.9990 chunk 79 optimal weight: 0.9980 chunk 81 optimal weight: 1.9990 chunk 146 optimal weight: 7.9990 chunk 144 optimal weight: 5.9990 chunk 125 optimal weight: 0.9990 chunk 54 optimal weight: 2.9990 chunk 14 optimal weight: 8.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 600 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4406 r_free = 0.4406 target = 0.223457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.192181 restraints weight = 17935.720| |-----------------------------------------------------------------------------| r_work (start): 0.4097 rms_B_bonded: 1.39 r_work: 0.3686 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work (final): 0.3686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.1352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16539 Z= 0.127 Angle : 0.493 8.056 22468 Z= 0.253 Chirality : 0.038 0.287 2746 Planarity : 0.004 0.060 2701 Dihedral : 6.860 77.765 2915 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 3.08 % Allowed : 26.25 % Favored : 70.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 2.16 (0.19), residues: 1982 helix: 2.30 (0.14), residues: 1378 sheet: 0.31 (0.53), residues: 96 loop : -0.84 (0.28), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B1112 HIS 0.004 0.001 HIS A 889 PHE 0.016 0.001 PHE B 201 TYR 0.016 0.001 TYR A 309 ARG 0.002 0.000 ARG A 500 Details of bonding type rmsd hydrogen bonds : bond 0.04565 ( 1082) hydrogen bonds : angle 3.82180 ( 3207) covalent geometry : bond 0.00296 (16539) covalent geometry : angle 0.49281 (22468) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3964 Ramachandran restraints generated. 1982 Oldfield, 0 Emsley, 1982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3964 Ramachandran restraints generated. 1982 Oldfield, 0 Emsley, 1982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 148 time to evaluate : 1.653 Fit side-chains REVERT: A 483 MET cc_start: 0.2990 (ttt) cc_final: 0.2726 (mtm) REVERT: A 651 LEU cc_start: 0.7106 (OUTLIER) cc_final: 0.6878 (pp) REVERT: A 1116 LYS cc_start: 0.7654 (tttm) cc_final: 0.7248 (tttm) REVERT: B 393 LEU cc_start: 0.8759 (OUTLIER) cc_final: 0.8536 (mm) REVERT: B 443 GLU cc_start: 0.7919 (OUTLIER) cc_final: 0.7422 (tm-30) REVERT: B 872 GLU cc_start: 0.6631 (OUTLIER) cc_final: 0.6415 (tp30) outliers start: 53 outliers final: 44 residues processed: 190 average time/residue: 0.2535 time to fit residues: 75.8394 Evaluate side-chains 193 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 145 time to evaluate : 1.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain A residue 234 SER Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 316 ASP Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 401 MET Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 640 ILE Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain A residue 844 ILE Chi-restraints excluded: chain A residue 872 GLU Chi-restraints excluded: chain A residue 924 GLU Chi-restraints excluded: chain A residue 989 VAL Chi-restraints excluded: chain A residue 1037 THR Chi-restraints excluded: chain A residue 1047 VAL Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain B residue 316 ASP Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 342 SER Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 401 MET Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain B residue 443 GLU Chi-restraints excluded: chain B residue 500 ARG Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 596 LYS Chi-restraints excluded: chain B residue 640 ILE Chi-restraints excluded: chain B residue 844 ILE Chi-restraints excluded: chain B residue 872 GLU Chi-restraints excluded: chain B residue 989 VAL Chi-restraints excluded: chain B residue 1037 THR Chi-restraints excluded: chain B residue 1047 VAL Chi-restraints excluded: chain B residue 1106 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 79 optimal weight: 0.1980 chunk 157 optimal weight: 7.9990 chunk 15 optimal weight: 3.9990 chunk 26 optimal weight: 0.3980 chunk 196 optimal weight: 9.9990 chunk 51 optimal weight: 0.0370 chunk 180 optimal weight: 9.9990 chunk 90 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 overall best weight: 0.9262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 600 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.218350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.195015 restraints weight = 17737.946| |-----------------------------------------------------------------------------| r_work (start): 0.4087 rms_B_bonded: 1.04 r_work: 0.3721 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3569 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.1398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 16539 Z= 0.109 Angle : 0.480 7.893 22468 Z= 0.247 Chirality : 0.038 0.283 2746 Planarity : 0.004 0.059 2701 Dihedral : 6.617 77.048 2915 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 2.74 % Allowed : 26.83 % Favored : 70.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 2.25 (0.19), residues: 1982 helix: 2.37 (0.14), residues: 1376 sheet: 0.40 (0.53), residues: 96 loop : -0.79 (0.27), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B1112 HIS 0.003 0.001 HIS A 889 PHE 0.015 0.001 PHE B 201 TYR 0.015 0.001 TYR A 309 ARG 0.002 0.000 ARG A 500 Details of bonding type rmsd hydrogen bonds : bond 0.04216 ( 1082) hydrogen bonds : angle 3.76437 ( 3207) covalent geometry : bond 0.00243 (16539) covalent geometry : angle 0.48025 (22468) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9727.89 seconds wall clock time: 176 minutes 49.20 seconds (10609.20 seconds total)