Starting phenix.real_space_refine on Sun Aug 24 01:41:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8u73_41967/08_2025/8u73_41967_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8u73_41967/08_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_41967/08_2025/8u73_41967.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8u73_41967/08_2025/8u73_41967.map" model { file = "/net/cci-nas-00/data/ceres_data/8u73_41967/08_2025/8u73_41967_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8u73_41967/08_2025/8u73_41967_neut.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.006 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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 4.42, per 1000 atoms: 0.27 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: 1.57 Conformation dependent library (CDL) restraints added in 718.7 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.61 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: 3.07 Time building geometry restraints manager: 2.05 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 1401 or (resid 1403 and (name C01 or name C02 o \ r name C03 or name C04 or name C05 or name C06 or name C07 or name C08 or name C \ 10 or name C11 or name C12 or name C13 or name C14 or name C15 or name C16 or na \ me C17 or name C18 or name C19 or name C20 or name C21 or name C22 or name C23 o \ r name C24 or name C26 or name C27 or name C28 or name C29 or name C30 or name C \ 32 or name C35 or name C36 or name C37 or name C38 or name C39 or name C41 or na \ me C55 or name C56 or name C57 or name C58 or name C59 or name C61 or name C80 o \ r name C81 or name C83 or name C85 or name O09 or name O25 or name O31 or name O \ 33 or name O34 or name O40 or name O42 or name O43 or name O44 or name O54 or na \ me O60 or name O63 or name O64 or name O76 or name O77 or name O78 or name O79 o \ r name O82 or name O84)))) selection = (chain 'B' and (resid 74 through 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: 3.410 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: 0.020 Extract box with map and model: 0.380 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 17.100 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.040 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:1.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.920 ------------------------------------------------------------------------------- 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 : 7.28 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.003 0.000 ARG B1169 TYR 0.013 0.001 TYR A 309 PHE 0.021 0.001 PHE B 201 TRP 0.035 0.001 TRP B1112 HIS 0.005 0.001 HIS A 889 Details of bonding type rmsd covalent geometry : bond 0.00378 (16539) covalent geometry : angle 0.71695 (22468) hydrogen bonds : bond 0.11828 ( 1082) hydrogen bonds : angle 5.64412 ( 3207) *********************** 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 : 0.658 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: 0.1170 time to fit residues: 30.1990 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 : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 98 optimal weight: 5.9990 chunk 194 optimal weight: 9.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 0.0970 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 0.8980 overall best weight: 1.1582 ------------------------------------------------------------------------------- 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 = 0.4311 r_free = 0.4311 target = 0.217748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.196650 restraints weight = 17497.509| |-----------------------------------------------------------------------------| r_work (start): 0.4113 rms_B_bonded: 1.03 r_work: 0.3705 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.3457 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.0726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16539 Z= 0.127 Angle : 0.526 7.980 22468 Z= 0.263 Chirality : 0.038 0.208 2746 Planarity : 0.004 0.063 2701 Dihedral : 8.532 108.630 2915 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 2.79 % Allowed : 24.04 % Favored : 73.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.65 (0.19), residues: 1982 helix: 1.99 (0.14), residues: 1366 sheet: 0.91 (0.63), residues: 76 loop : -1.27 (0.25), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 583 TYR 0.017 0.001 TYR A 309 PHE 0.017 0.001 PHE B 201 TRP 0.014 0.001 TRP B1112 HIS 0.003 0.001 HIS B 928 Details of bonding type rmsd covalent geometry : bond 0.00285 (16539) covalent geometry : angle 0.52579 (22468) hydrogen bonds : bond 0.04830 ( 1082) hydrogen bonds : angle 4.19314 ( 3207) *********************** 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 208 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 160 time to evaluate : 0.522 Fit side-chains REVERT: A 651 LEU cc_start: 0.7066 (OUTLIER) cc_final: 0.6803 (pp) REVERT: A 872 GLU cc_start: 0.6922 (OUTLIER) cc_final: 0.6659 (tp30) REVERT: A 928 HIS cc_start: 0.7523 (m90) cc_final: 0.7319 (m90) REVERT: B 393 LEU cc_start: 0.8811 (OUTLIER) cc_final: 0.8573 (mm) REVERT: B 872 GLU cc_start: 0.6994 (OUTLIER) cc_final: 0.6767 (tp30) outliers start: 48 outliers final: 21 residues processed: 199 average time/residue: 0.0992 time to fit residues: 31.4094 Evaluate side-chains 173 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 148 time to evaluate : 0.408 ------------------------------------------------------------------------------- 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 277 LEU Chi-restraints excluded: chain A residue 327 VAL 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 205 MET Chi-restraints excluded: chain B residue 321 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 26 optimal weight: 0.0980 chunk 61 optimal weight: 20.0000 chunk 85 optimal weight: 0.9990 chunk 161 optimal weight: 20.0000 chunk 132 optimal weight: 2.9990 chunk 95 optimal weight: 8.9990 chunk 183 optimal weight: 3.9990 chunk 151 optimal weight: 9.9990 chunk 107 optimal weight: 1.9990 chunk 86 optimal weight: 8.9990 chunk 179 optimal weight: 6.9990 overall best weight: 2.0188 ------------------------------------------------------------------------------- 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 = 0.4287 r_free = 0.4287 target = 0.215110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.194095 restraints weight = 17724.867| |-----------------------------------------------------------------------------| r_work (start): 0.4097 rms_B_bonded: 1.08 r_work: 0.3676 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3479 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.0941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 16539 Z= 0.167 Angle : 0.543 8.677 22468 Z= 0.276 Chirality : 0.040 0.357 2746 Planarity : 0.004 0.061 2701 Dihedral : 8.075 109.435 2915 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 3.55 % Allowed : 24.62 % Favored : 71.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.69 (0.19), residues: 1982 helix: 2.03 (0.14), residues: 1362 sheet: 0.87 (0.62), residues: 76 loop : -1.27 (0.26), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 500 TYR 0.018 0.001 TYR A 309 PHE 0.017 0.001 PHE B 201 TRP 0.018 0.002 TRP B1112 HIS 0.006 0.001 HIS B 889 Details of bonding type rmsd covalent geometry : bond 0.00402 (16539) covalent geometry : angle 0.54281 (22468) hydrogen bonds : bond 0.05494 ( 1082) hydrogen bonds : angle 4.17314 ( 3207) *********************** 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 223 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 162 time to evaluate : 0.617 Fit side-chains REVERT: A 587 LEU cc_start: 0.8558 (OUTLIER) cc_final: 0.8357 (mp) REVERT: A 651 LEU cc_start: 0.7048 (OUTLIER) cc_final: 0.6764 (pp) REVERT: A 872 GLU cc_start: 0.6870 (OUTLIER) cc_final: 0.6627 (tp30) REVERT: B 393 LEU cc_start: 0.8825 (OUTLIER) cc_final: 0.8589 (mm) REVERT: B 443 GLU cc_start: 0.8087 (OUTLIER) cc_final: 0.7605 (tm-30) REVERT: B 872 GLU cc_start: 0.6938 (OUTLIER) cc_final: 0.6717 (tp30) outliers start: 61 outliers final: 33 residues processed: 211 average time/residue: 0.0920 time to fit residues: 30.8396 Evaluate side-chains 187 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 148 time to evaluate : 0.405 ------------------------------------------------------------------------------- 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 316 ASP Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 370 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 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 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 260 THR 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 443 GLU 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 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 11 optimal weight: 5.9990 chunk 51 optimal weight: 4.9990 chunk 158 optimal weight: 8.9990 chunk 150 optimal weight: 0.9990 chunk 91 optimal weight: 1.9990 chunk 148 optimal weight: 0.7980 chunk 198 optimal weight: 9.9990 chunk 133 optimal weight: 9.9990 chunk 80 optimal weight: 9.9990 chunk 48 optimal weight: 0.6980 chunk 180 optimal weight: 20.0000 overall best weight: 1.8986 ------------------------------------------------------------------------------- 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 = 0.4287 r_free = 0.4287 target = 0.215668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.191289 restraints weight = 17764.086| |-----------------------------------------------------------------------------| r_work (start): 0.4052 rms_B_bonded: 1.10 r_work: 0.3658 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3491 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.1061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 16539 Z= 0.159 Angle : 0.513 7.741 22468 Z= 0.265 Chirality : 0.039 0.158 2746 Planarity : 0.004 0.061 2701 Dihedral : 7.923 112.369 2915 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 3.84 % Allowed : 25.09 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.77 (0.19), residues: 1982 helix: 2.10 (0.14), residues: 1362 sheet: 0.92 (0.62), residues: 76 loop : -1.26 (0.26), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 500 TYR 0.017 0.001 TYR B 309 PHE 0.017 0.001 PHE B 201 TRP 0.016 0.002 TRP B1112 HIS 0.005 0.001 HIS B 889 Details of bonding type rmsd covalent geometry : bond 0.00384 (16539) covalent geometry : angle 0.51317 (22468) hydrogen bonds : bond 0.05257 ( 1082) hydrogen bonds : angle 4.05285 ( 3207) *********************** 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 222 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 156 time to evaluate : 0.587 Fit side-chains REVERT: A 651 LEU cc_start: 0.7020 (OUTLIER) cc_final: 0.6766 (pp) REVERT: A 872 GLU cc_start: 0.6966 (OUTLIER) cc_final: 0.6734 (tp30) REVERT: B 393 LEU cc_start: 0.8825 (OUTLIER) cc_final: 0.8594 (mm) REVERT: B 443 GLU cc_start: 0.8090 (OUTLIER) cc_final: 0.7628 (tm-30) REVERT: B 872 GLU cc_start: 0.7023 (OUTLIER) cc_final: 0.6778 (tp30) outliers start: 66 outliers final: 38 residues processed: 209 average time/residue: 0.0982 time to fit residues: 32.5282 Evaluate side-chains 193 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 150 time to evaluate : 0.461 ------------------------------------------------------------------------------- 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 316 ASP Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 338 LYS Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 401 MET Chi-restraints excluded: chain A residue 424 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 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 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 443 GLU 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 854 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 163 optimal weight: 30.0000 chunk 185 optimal weight: 1.9990 chunk 129 optimal weight: 0.6980 chunk 194 optimal weight: 3.9990 chunk 29 optimal weight: 0.7980 chunk 93 optimal weight: 6.9990 chunk 126 optimal weight: 5.9990 chunk 88 optimal weight: 10.0000 chunk 160 optimal weight: 0.0170 chunk 84 optimal weight: 0.9980 chunk 170 optimal weight: 2.9990 overall best weight: 0.9020 ------------------------------------------------------------------------------- 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 = 0.217566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.192030 restraints weight = 17732.663| |-----------------------------------------------------------------------------| r_work (start): 0.4065 rms_B_bonded: 1.14 r_work: 0.3683 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3509 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.1110 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= 0.108 Angle : 0.476 8.946 22468 Z= 0.244 Chirality : 0.038 0.328 2746 Planarity : 0.004 0.059 2701 Dihedral : 7.510 110.315 2915 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 2.85 % Allowed : 26.14 % Favored : 71.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.05 (0.19), residues: 1982 helix: 2.29 (0.14), residues: 1366 sheet: 0.16 (0.55), residues: 96 loop : -1.00 (0.27), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 609 TYR 0.015 0.001 TYR B 309 PHE 0.015 0.001 PHE B 201 TRP 0.015 0.001 TRP B1112 HIS 0.004 0.001 HIS A 889 Details of bonding type rmsd covalent geometry : bond 0.00237 (16539) covalent geometry : angle 0.47600 (22468) hydrogen bonds : bond 0.04353 ( 1082) hydrogen bonds : angle 3.88197 ( 3207) *********************** 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 209 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 160 time to evaluate : 0.385 Fit side-chains REVERT: A 651 LEU cc_start: 0.7018 (OUTLIER) cc_final: 0.6769 (pp) REVERT: A 872 GLU cc_start: 0.6987 (OUTLIER) cc_final: 0.6755 (tp30) REVERT: B 393 LEU cc_start: 0.8786 (OUTLIER) cc_final: 0.8546 (mm) REVERT: B 443 GLU cc_start: 0.8104 (OUTLIER) cc_final: 0.7665 (tm-30) REVERT: B 525 ILE cc_start: 0.9060 (OUTLIER) cc_final: 0.8844 (mp) REVERT: B 872 GLU cc_start: 0.7080 (OUTLIER) cc_final: 0.6859 (tp30) REVERT: B 1112 TRP cc_start: 0.6850 (m100) cc_final: 0.6437 (m100) outliers start: 49 outliers final: 34 residues processed: 198 average time/residue: 0.1003 time to fit residues: 30.8508 Evaluate side-chains 190 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 150 time to evaluate : 0.449 ------------------------------------------------------------------------------- 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 321 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 872 GLU Chi-restraints excluded: chain A residue 989 VAL Chi-restraints excluded: chain A residue 1002 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 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 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 872 GLU Chi-restraints excluded: chain B residue 989 VAL Chi-restraints excluded: chain B residue 1002 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 74 optimal weight: 2.9990 chunk 93 optimal weight: 0.0770 chunk 5 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 75 optimal weight: 3.9990 chunk 64 optimal weight: 10.0000 chunk 7 optimal weight: 1.9990 chunk 119 optimal weight: 3.9990 chunk 46 optimal weight: 0.0070 chunk 128 optimal weight: 0.5980 chunk 124 optimal weight: 0.3980 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 237 ASN B 877 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.218728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.191974 restraints weight = 17687.997| |-----------------------------------------------------------------------------| r_work (start): 0.4064 rms_B_bonded: 1.17 r_work: 0.3693 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3601 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.1231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 16539 Z= 0.098 Angle : 0.452 7.642 22468 Z= 0.234 Chirality : 0.037 0.167 2746 Planarity : 0.004 0.059 2701 Dihedral : 7.214 105.642 2915 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 3.20 % Allowed : 26.31 % Favored : 70.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.23 (0.19), residues: 1982 helix: 2.44 (0.14), residues: 1370 sheet: 0.22 (0.54), residues: 96 loop : -1.01 (0.27), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 500 TYR 0.014 0.001 TYR A 309 PHE 0.014 0.001 PHE B 201 TRP 0.011 0.001 TRP A 318 HIS 0.003 0.000 HIS B 889 Details of bonding type rmsd covalent geometry : bond 0.00204 (16539) covalent geometry : angle 0.45237 (22468) hydrogen bonds : bond 0.03943 ( 1082) hydrogen bonds : angle 3.77720 ( 3207) *********************** 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 213 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 158 time to evaluate : 0.607 Fit side-chains REVERT: A 443 GLU cc_start: 0.7934 (OUTLIER) cc_final: 0.7540 (tm-30) REVERT: A 525 ILE cc_start: 0.8973 (OUTLIER) cc_final: 0.8683 (mp) REVERT: A 651 LEU cc_start: 0.6952 (OUTLIER) cc_final: 0.6715 (pp) REVERT: A 872 GLU cc_start: 0.6793 (OUTLIER) cc_final: 0.6562 (tp30) REVERT: B 393 LEU cc_start: 0.8748 (OUTLIER) cc_final: 0.8492 (mm) REVERT: B 443 GLU cc_start: 0.7957 (OUTLIER) cc_final: 0.7511 (tm-30) REVERT: B 872 GLU cc_start: 0.6821 (OUTLIER) cc_final: 0.6607 (tp30) REVERT: B 1112 TRP cc_start: 0.6804 (m100) cc_final: 0.6485 (m100) outliers start: 55 outliers final: 35 residues processed: 203 average time/residue: 0.1034 time to fit residues: 33.0232 Evaluate side-chains 192 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 150 time to evaluate : 0.609 ------------------------------------------------------------------------------- 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 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 443 GLU Chi-restraints excluded: chain A residue 525 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 872 GLU Chi-restraints excluded: chain A residue 941 LEU 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 164 optimal weight: 0.0570 chunk 91 optimal weight: 6.9990 chunk 80 optimal weight: 5.9990 chunk 13 optimal weight: 4.9990 chunk 12 optimal weight: 1.9990 chunk 83 optimal weight: 7.9990 chunk 120 optimal weight: 0.9980 chunk 98 optimal weight: 2.9990 chunk 189 optimal weight: 2.9990 chunk 135 optimal weight: 0.8980 chunk 144 optimal weight: 6.9990 overall best weight: 1.3902 ------------------------------------------------------------------------------- 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 = 0.4300 r_free = 0.4300 target = 0.217192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.193272 restraints weight = 17595.938| |-----------------------------------------------------------------------------| r_work (start): 0.4071 rms_B_bonded: 1.06 r_work: 0.3680 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3589 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.3589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.1242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16539 Z= 0.130 Angle : 0.502 11.105 22468 Z= 0.254 Chirality : 0.039 0.378 2746 Planarity : 0.004 0.060 2701 Dihedral : 7.362 100.393 2915 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 3.49 % Allowed : 25.96 % Favored : 70.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.17 (0.19), residues: 1982 helix: 2.39 (0.14), residues: 1366 sheet: 0.24 (0.54), residues: 96 loop : -0.97 (0.27), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 500 TYR 0.017 0.001 TYR B 309 PHE 0.016 0.001 PHE B 201 TRP 0.013 0.001 TRP A 318 HIS 0.004 0.001 HIS B 889 Details of bonding type rmsd covalent geometry : bond 0.00305 (16539) covalent geometry : angle 0.50176 (22468) hydrogen bonds : bond 0.04556 ( 1082) hydrogen bonds : angle 3.84150 ( 3207) *********************** 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 215 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 155 time to evaluate : 0.594 Fit side-chains REVERT: A 443 GLU cc_start: 0.7929 (OUTLIER) cc_final: 0.7503 (tm-30) REVERT: A 651 LEU cc_start: 0.6946 (OUTLIER) cc_final: 0.6707 (pp) REVERT: A 872 GLU cc_start: 0.6734 (OUTLIER) cc_final: 0.6507 (tp30) REVERT: B 393 LEU cc_start: 0.8764 (OUTLIER) cc_final: 0.8508 (mm) REVERT: B 443 GLU cc_start: 0.7921 (OUTLIER) cc_final: 0.7454 (tm-30) REVERT: B 506 ASN cc_start: 0.8108 (t0) cc_final: 0.7717 (m-40) REVERT: B 525 ILE cc_start: 0.9045 (OUTLIER) cc_final: 0.8826 (mp) REVERT: B 872 GLU cc_start: 0.6785 (OUTLIER) cc_final: 0.6570 (tp30) REVERT: B 1112 TRP cc_start: 0.6817 (m100) cc_final: 0.6463 (m100) outliers start: 60 outliers final: 44 residues processed: 205 average time/residue: 0.1081 time to fit residues: 34.5487 Evaluate side-chains 203 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 152 time to evaluate : 0.490 ------------------------------------------------------------------------------- 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 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 443 GLU 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 1002 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 338 LYS 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 760 VAL 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 1002 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 41 optimal weight: 30.0000 chunk 59 optimal weight: 10.0000 chunk 62 optimal weight: 0.0970 chunk 133 optimal weight: 0.1980 chunk 132 optimal weight: 7.9990 chunk 164 optimal weight: 2.9990 chunk 106 optimal weight: 0.9980 chunk 173 optimal weight: 0.6980 chunk 191 optimal weight: 6.9990 chunk 99 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- 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 = 0.4321 r_free = 0.4321 target = 0.219602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.194122 restraints weight = 17720.454| |-----------------------------------------------------------------------------| r_work (start): 0.4070 rms_B_bonded: 1.13 r_work: 0.3687 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work (final): 0.3687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.1359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 16539 Z= 0.096 Angle : 0.461 8.346 22468 Z= 0.235 Chirality : 0.037 0.303 2746 Planarity : 0.004 0.059 2701 Dihedral : 6.930 87.284 2915 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 3.14 % Allowed : 26.02 % Favored : 70.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.31 (0.19), residues: 1982 helix: 2.50 (0.14), residues: 1368 sheet: 0.25 (0.53), residues: 96 loop : -0.96 (0.27), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 500 TYR 0.012 0.001 TYR A 309 PHE 0.014 0.001 PHE B 201 TRP 0.010 0.001 TRP A 318 HIS 0.002 0.000 HIS B 889 Details of bonding type rmsd covalent geometry : bond 0.00202 (16539) covalent geometry : angle 0.46068 (22468) hydrogen bonds : bond 0.03804 ( 1082) hydrogen bonds : angle 3.71661 ( 3207) *********************** 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 212 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 158 time to evaluate : 0.552 Fit side-chains REVERT: A 443 GLU cc_start: 0.7714 (OUTLIER) cc_final: 0.7327 (tm-30) REVERT: A 651 LEU cc_start: 0.6948 (OUTLIER) cc_final: 0.6728 (pp) REVERT: A 841 LYS cc_start: 0.8312 (OUTLIER) cc_final: 0.7751 (tttt) REVERT: A 872 GLU cc_start: 0.6486 (OUTLIER) cc_final: 0.6257 (tp30) REVERT: B 393 LEU cc_start: 0.8702 (OUTLIER) cc_final: 0.8445 (mm) REVERT: B 443 GLU cc_start: 0.7689 (OUTLIER) cc_final: 0.7222 (tm-30) REVERT: B 841 LYS cc_start: 0.8309 (OUTLIER) cc_final: 0.7751 (tttt) REVERT: B 872 GLU cc_start: 0.6509 (OUTLIER) cc_final: 0.6292 (tp30) REVERT: B 1085 SER cc_start: 0.6918 (OUTLIER) cc_final: 0.6579 (p) REVERT: B 1112 TRP cc_start: 0.6719 (m100) cc_final: 0.6422 (m100) outliers start: 54 outliers final: 36 residues processed: 202 average time/residue: 0.1078 time to fit residues: 33.9876 Evaluate side-chains 194 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 149 time to evaluate : 0.612 ------------------------------------------------------------------------------- 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 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 401 MET Chi-restraints excluded: chain A residue 443 GLU 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 841 LYS 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 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 640 ILE Chi-restraints excluded: chain B residue 760 VAL Chi-restraints excluded: chain B residue 841 LYS 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 1085 SER 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 189 optimal weight: 4.9990 chunk 115 optimal weight: 6.9990 chunk 23 optimal weight: 0.8980 chunk 72 optimal weight: 0.5980 chunk 191 optimal weight: 5.9990 chunk 140 optimal weight: 3.9990 chunk 31 optimal weight: 5.9990 chunk 165 optimal weight: 0.7980 chunk 58 optimal weight: 8.9990 chunk 129 optimal weight: 1.9990 chunk 33 optimal weight: 5.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 917 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.216620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.193103 restraints weight = 17661.717| |-----------------------------------------------------------------------------| r_work (start): 0.4057 rms_B_bonded: 1.08 r_work: 0.3701 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3601 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.3601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.1345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 16539 Z= 0.144 Angle : 0.514 7.884 22468 Z= 0.261 Chirality : 0.039 0.272 2746 Planarity : 0.004 0.061 2701 Dihedral : 7.051 78.479 2915 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.85 % Allowed : 26.66 % Favored : 70.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.19 (0.19), residues: 1982 helix: 2.39 (0.14), residues: 1366 sheet: 0.27 (0.53), residues: 96 loop : -0.94 (0.27), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 500 TYR 0.018 0.001 TYR A 309 PHE 0.017 0.001 PHE B 201 TRP 0.013 0.001 TRP A 318 HIS 0.004 0.001 HIS A1120 Details of bonding type rmsd covalent geometry : bond 0.00346 (16539) covalent geometry : angle 0.51389 (22468) hydrogen bonds : bond 0.04778 ( 1082) hydrogen bonds : angle 3.83422 ( 3207) *********************** 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 204 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 155 time to evaluate : 0.633 Fit side-chains REVERT: A 443 GLU cc_start: 0.7906 (OUTLIER) cc_final: 0.7486 (tm-30) REVERT: A 483 MET cc_start: 0.2757 (ttt) cc_final: 0.2543 (mtm) REVERT: A 506 ASN cc_start: 0.7981 (t0) cc_final: 0.7607 (m-40) REVERT: A 651 LEU cc_start: 0.6838 (OUTLIER) cc_final: 0.6604 (pp) REVERT: A 872 GLU cc_start: 0.6769 (OUTLIER) cc_final: 0.6549 (tp30) REVERT: B 393 LEU cc_start: 0.8742 (OUTLIER) cc_final: 0.8485 (mm) REVERT: B 443 GLU cc_start: 0.7880 (OUTLIER) cc_final: 0.7410 (tm-30) REVERT: B 483 MET cc_start: 0.2775 (ttt) cc_final: 0.2540 (mtm) REVERT: B 506 ASN cc_start: 0.8079 (t0) cc_final: 0.7703 (m-40) REVERT: B 872 GLU cc_start: 0.6812 (OUTLIER) cc_final: 0.6604 (tp30) REVERT: B 1085 SER cc_start: 0.6970 (OUTLIER) cc_final: 0.6618 (p) REVERT: B 1112 TRP cc_start: 0.6790 (m100) cc_final: 0.6484 (m100) outliers start: 49 outliers final: 37 residues processed: 194 average time/residue: 0.1156 time to fit residues: 35.3571 Evaluate side-chains 191 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 147 time to evaluate : 0.626 ------------------------------------------------------------------------------- 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 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 443 GLU 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 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 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 760 VAL 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 1085 SER 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 19 optimal weight: 3.9990 chunk 30 optimal weight: 0.7980 chunk 126 optimal weight: 0.1980 chunk 139 optimal weight: 0.8980 chunk 53 optimal weight: 3.9990 chunk 123 optimal weight: 0.9990 chunk 102 optimal weight: 0.0670 chunk 124 optimal weight: 0.9990 chunk 188 optimal weight: 8.9990 chunk 84 optimal weight: 0.5980 chunk 9 optimal weight: 0.9990 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 917 GLN B 600 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.219753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.195586 restraints weight = 17759.051| |-----------------------------------------------------------------------------| r_work (start): 0.4084 rms_B_bonded: 1.15 r_work: 0.3784 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3723 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.3723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.1429 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= 0.098 Angle : 0.478 12.330 22468 Z= 0.242 Chirality : 0.038 0.431 2746 Planarity : 0.004 0.059 2701 Dihedral : 6.537 76.419 2915 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 2.62 % Allowed : 27.18 % Favored : 70.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.33 (0.19), residues: 1982 helix: 2.51 (0.14), residues: 1368 sheet: 0.31 (0.53), residues: 96 loop : -0.94 (0.27), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 500 TYR 0.012 0.001 TYR B 309 PHE 0.014 0.001 PHE B 201 TRP 0.011 0.001 TRP A 318 HIS 0.003 0.001 HIS A1120 Details of bonding type rmsd covalent geometry : bond 0.00203 (16539) covalent geometry : angle 0.47839 (22468) hydrogen bonds : bond 0.03825 ( 1082) hydrogen bonds : angle 3.72591 ( 3207) ********************** 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 200 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 155 time to evaluate : 0.554 Fit side-chains REVERT: A 443 GLU cc_start: 0.7800 (OUTLIER) cc_final: 0.7422 (tm-30) REVERT: A 651 LEU cc_start: 0.6648 (OUTLIER) cc_final: 0.6438 (pp) REVERT: B 393 LEU cc_start: 0.8679 (OUTLIER) cc_final: 0.8413 (mm) REVERT: B 443 GLU cc_start: 0.7798 (OUTLIER) cc_final: 0.7340 (tm-30) REVERT: B 1112 TRP cc_start: 0.6723 (m100) cc_final: 0.6491 (m100) outliers start: 45 outliers final: 36 residues processed: 191 average time/residue: 0.1155 time to fit residues: 34.7789 Evaluate side-chains 187 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 147 time to evaluate : 0.657 ------------------------------------------------------------------------------- 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 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 443 GLU 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 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 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 760 VAL 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 1057 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 75 optimal weight: 10.0000 chunk 99 optimal weight: 0.1980 chunk 33 optimal weight: 6.9990 chunk 39 optimal weight: 0.8980 chunk 66 optimal weight: 0.9980 chunk 95 optimal weight: 8.9990 chunk 4 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 chunk 113 optimal weight: 5.9990 chunk 89 optimal weight: 0.8980 chunk 183 optimal weight: 10.0000 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 600 HIS B 928 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.219081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.193586 restraints weight = 17654.981| |-----------------------------------------------------------------------------| r_work (start): 0.4081 rms_B_bonded: 1.14 r_work: 0.3676 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work (final): 0.3676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.1499 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= 0.103 Angle : 0.483 11.964 22468 Z= 0.243 Chirality : 0.038 0.386 2746 Planarity : 0.004 0.060 2701 Dihedral : 6.396 76.445 2915 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 2.68 % Allowed : 27.24 % Favored : 70.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.35 (0.19), residues: 1982 helix: 2.50 (0.14), residues: 1370 sheet: 0.32 (0.53), residues: 96 loop : -0.88 (0.27), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 500 TYR 0.015 0.001 TYR A 309 PHE 0.015 0.001 PHE B 598 TRP 0.011 0.001 TRP A 318 HIS 0.008 0.001 HIS B 928 Details of bonding type rmsd covalent geometry : bond 0.00225 (16539) covalent geometry : angle 0.48259 (22468) hydrogen bonds : bond 0.03915 ( 1082) hydrogen bonds : angle 3.71355 ( 3207) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3404.23 seconds wall clock time: 59 minutes 4.46 seconds (3544.46 seconds total)