Starting phenix.real_space_refine on Fri Jul 3 22:01:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8otx_17186/07_2026/8otx_17186_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8otx_17186/07_2026/8otx_17186.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.08 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8otx_17186/07_2026/8otx_17186_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8otx_17186/07_2026/8otx_17186_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8otx_17186/07_2026/8otx_17186.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8otx_17186/07_2026/8otx_17186.map" } resolution = 3.08 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.016 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 4 5.49 5 S 74 5.16 5 C 10344 2.51 5 N 2668 2.21 5 O 2876 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15966 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 7889 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1054, 7882 Classifications: {'peptide': 1054} Incomplete info: {'truncation_to_alanine': 127} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 1023} Chain breaks: 3 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 460 Unresolved non-hydrogen angles: 586 Unresolved non-hydrogen dihedrals: 381 Unresolved non-hydrogen chiralities: 58 Planarities with less than four sites: {'GLU:plan': 6, 'TYR:plan': 5, 'HIS:plan': 4, 'PHE:plan': 7, 'ASN:plan1': 5, 'GLN:plan1': 2, 'ASP:plan': 4, 'ARG:plan': 6, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 195 Conformer: "B" Number of residues, atoms: 1054, 7882 Classifications: {'peptide': 1054} Incomplete info: {'truncation_to_alanine': 127} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 1023} Chain breaks: 3 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 460 Unresolved non-hydrogen angles: 586 Unresolved non-hydrogen dihedrals: 381 Unresolved non-hydrogen chiralities: 58 Planarities with less than four sites: {'GLU:plan': 6, 'TYR:plan': 5, 'HIS:plan': 4, 'PHE:plan': 7, 'ASN:plan1': 5, 'GLN:plan1': 2, 'ASP:plan': 4, 'ARG:plan': 6, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 195 bond proxies already assigned to first conformer: 8013 Chain: "A" Number of atoms: 7889 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1054, 7882 Classifications: {'peptide': 1054} Incomplete info: {'truncation_to_alanine': 127} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 1023} Chain breaks: 3 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 460 Unresolved non-hydrogen angles: 586 Unresolved non-hydrogen dihedrals: 381 Unresolved non-hydrogen chiralities: 58 Planarities with less than four sites: {'GLU:plan': 6, 'TYR:plan': 5, 'HIS:plan': 4, 'PHE:plan': 7, 'ASN:plan1': 5, 'GLN:plan1': 2, 'ASP:plan': 4, 'ARG:plan': 6, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 195 Conformer: "B" Number of residues, atoms: 1054, 7882 Classifications: {'peptide': 1054} Incomplete info: {'truncation_to_alanine': 127} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 1023} Chain breaks: 3 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 460 Unresolved non-hydrogen angles: 586 Unresolved non-hydrogen dihedrals: 381 Unresolved non-hydrogen chiralities: 58 Planarities with less than four sites: {'GLU:plan': 6, 'TYR:plan': 5, 'HIS:plan': 4, 'PHE:plan': 7, 'ASN:plan1': 5, 'GLN:plan1': 2, 'ASP:plan': 4, 'ARG:plan': 6, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 195 bond proxies already assigned to first conformer: 8013 Chain: "B" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 93 Unusual residues: {'3PH': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "A" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 93 Unusual residues: {'3PH': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 5.19, per 1000 atoms: 0.33 Number of scatterers: 15966 At special positions: 0 Unit cell: (150.76, 106.903, 123.349, 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 74 16.00 P 4 15.00 O 2876 8.00 N 2668 7.00 C 10344 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: 1.38 Conformation dependent library (CDL) restraints added in 1.1 seconds 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3980 Finding SS restraints... Secondary structure from input PDB file: 82 helices and 8 sheets defined 72.4% alpha, 3.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'B' and resid 76 through 95 removed outlier: 3.670A pdb=" N PHE B 80 " --> pdb=" O LYS B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 120 removed outlier: 3.980A pdb=" N VAL B 105 " --> pdb=" O PRO B 101 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ASN B 119 " --> pdb=" O VAL B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 126 removed outlier: 3.597A pdb=" N GLU B 124 " --> pdb=" O VAL B 120 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLU B 125 " --> pdb=" O PRO B 121 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N HIS B 126 " --> pdb=" O LEU B 122 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 120 through 126' Processing helix chain 'B' and resid 134 through 154 Proline residue: B 144 - end of helix Processing helix chain 'B' and resid 155 through 162 removed outlier: 3.626A pdb=" N SER B 162 " --> pdb=" O THR B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 189 Processing helix chain 'B' and resid 194 through 206 Processing helix chain 'B' and resid 210 through 220 removed outlier: 3.777A pdb=" N VAL B 214 " --> pdb=" O PRO B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 254 Processing helix chain 'B' and resid 260 through 291 removed outlier: 4.549A pdb=" N GLY B 275 " --> pdb=" O VAL B 271 " (cutoff:3.500A) Proline residue: B 276 - end of helix Processing helix chain 'B' and resid 296 through 317 removed outlier: 3.686A pdb=" N GLU B 300 " --> pdb=" O ASP B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 337 Processing helix chain 'B' and resid 342 through 376 removed outlier: 3.704A pdb=" N ARG B 351 " --> pdb=" O VAL B 347 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLY B 369 " --> pdb=" O PHE B 365 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N VAL B 370 " --> pdb=" O MET B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 377 through 379 No H-bonds generated for 'chain 'B' and resid 377 through 379' Processing helix chain 'B' and resid 381 through 413 removed outlier: 4.375A pdb=" N TRP B 385 " --> pdb=" O ASP B 381 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N PHE B 386 " --> pdb=" O LYS B 382 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLY B 400 " --> pdb=" O THR B 396 " (cutoff:3.500A) Proline residue: B 408 - end of helix Processing helix chain 'B' and resid 418 through 428 Processing helix chain 'B' and resid 432 through 446 removed outlier: 3.998A pdb=" N LEU B 436 " --> pdb=" O GLY B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 481 removed outlier: 5.407A pdb=" N LYS B 454 " --> pdb=" O VAL B 450 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N PHE B 455 " --> pdb=" O ILE B 451 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU B 456 " --> pdb=" O GLY B 452 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ALA B 471 " --> pdb=" O LEU B 467 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N THR B 472 " --> pdb=" O VAL B 468 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N GLN B 475 " --> pdb=" O ALA B 471 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N THR B 476 " --> pdb=" O THR B 472 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 515 Processing helix chain 'B' and resid 524 through 529 Processing helix chain 'B' and resid 574 through 600 Processing helix chain 'B' and resid 605 through 621 Processing helix chain 'B' and resid 634 through 639 Processing helix chain 'B' and resid 641 through 654 removed outlier: 3.818A pdb=" N LYS B 645 " --> pdb=" O TYR B 641 " (cutoff:3.500A) Processing helix chain 'B' and resid 668 through 677 Processing helix chain 'B' and resid 677 through 704 removed outlier: 3.919A pdb=" N GLU B 681 " --> pdb=" O HIS B 677 " (cutoff:3.500A) removed outlier: 3.570A 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 724 through 750 Processing helix chain 'B' and resid 756 through 761 removed outlier: 3.810A pdb=" N SER B 761 " --> pdb=" O HIS B 757 " (cutoff:3.500A) Processing helix chain 'B' and resid 761 through 783 removed outlier: 3.806A pdb=" N LYS B 765 " --> pdb=" O SER B 761 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N PHE B 766 " --> pdb=" O HIS B 762 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASP B 767 " --> pdb=" O TRP B 763 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N THR B 783 " --> pdb=" O ILE B 779 " (cutoff:3.500A) Processing helix chain 'B' and resid 799 through 806 removed outlier: 4.503A pdb=" N LEU B 804 " --> pdb=" O LEU B 801 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N LEU B 805 " --> pdb=" O PHE B 802 " (cutoff:3.500A) Processing helix chain 'B' and resid 807 through 812 removed outlier: 3.915A pdb=" N LEU B 811 " --> pdb=" O GLY B 807 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ARG B 812 " --> pdb=" O LEU B 808 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 807 through 812' Processing helix chain 'B' and resid 813 through 857 Proline residue: B 819 - end of helix Processing helix chain 'B' and resid 863 through 889 removed outlier: 4.003A pdb=" N ILE B 870 " --> pdb=" O GLU B 866 " (cutoff:3.500A) Processing helix chain 'B' and resid 889 through 919 removed outlier: 3.982A pdb=" N ALA B 893 " --> pdb=" O HIS B 889 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N VAL B 894 " --> pdb=" O PRO B 890 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N SER B 895 " --> pdb=" O GLY B 891 " (cutoff:3.500A) Processing helix chain 'B' and resid 923 through 943 removed outlier: 3.610A pdb=" N ASN B 943 " --> pdb=" O LYS B 939 " (cutoff:3.500A) Processing helix chain 'B' and resid 952 through 959 Processing helix chain 'B' and resid 966 through 976 removed outlier: 3.647A pdb=" N ILE B 970 " --> pdb=" O ASP B 966 " (cutoff:3.500A) Processing helix chain 'B' and resid 1043 through 1050 Processing helix chain 'B' and resid 1069 through 1080 Processing helix chain 'B' and resid 1085 through 1107 removed outlier: 3.696A pdb=" N THR B1100 " --> pdb=" O ILE B1096 " (cutoff:3.500A) Proline residue: B1101 - end of helix Processing helix chain 'B' and resid 1115 through 1123 removed outlier: 3.621A pdb=" N ARG B1123 " --> pdb=" O LEU B1119 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 95 removed outlier: 3.665A pdb=" N PHE A 80 " --> pdb=" O LYS A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 120 removed outlier: 3.985A pdb=" N VAL A 105 " --> pdb=" O PRO A 101 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ASN A 119 " --> pdb=" O VAL A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 126 removed outlier: 3.601A pdb=" N GLU A 124 " --> pdb=" O VAL A 120 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLU A 125 " --> pdb=" O PRO A 121 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N HIS A 126 " --> pdb=" O LEU A 122 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 120 through 126' Processing helix chain 'A' and resid 134 through 154 Proline residue: A 144 - end of helix Processing helix chain 'A' and resid 155 through 162 removed outlier: 3.628A pdb=" N SER A 162 " --> pdb=" O THR A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 189 Processing helix chain 'A' and resid 194 through 206 Processing helix chain 'A' and resid 210 through 220 removed outlier: 3.736A pdb=" N VAL A 214 " --> pdb=" O PRO A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 254 Processing helix chain 'A' and resid 260 through 291 removed outlier: 4.550A pdb=" N GLY A 275 " --> pdb=" O VAL A 271 " (cutoff:3.500A) Proline residue: A 276 - end of helix Processing helix chain 'A' and resid 296 through 317 removed outlier: 3.687A pdb=" N GLU A 300 " --> pdb=" O ASP A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 337 Processing helix chain 'A' and resid 342 through 376 removed outlier: 3.706A pdb=" N ARG A 351 " --> pdb=" O VAL A 347 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLY A 369 " --> pdb=" O PHE A 365 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL A 370 " --> pdb=" O MET A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 379 No H-bonds generated for 'chain 'A' and resid 377 through 379' Processing helix chain 'A' and resid 381 through 413 removed outlier: 4.394A pdb=" N TRP A 385 " --> pdb=" O ASP A 381 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N PHE A 386 " --> pdb=" O LYS A 382 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLY A 400 " --> pdb=" O THR A 396 " (cutoff:3.500A) Proline residue: A 408 - end of helix Processing helix chain 'A' and resid 418 through 428 Processing helix chain 'A' and resid 432 through 446 removed outlier: 4.052A pdb=" N LEU A 436 " --> pdb=" O GLY A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 481 removed outlier: 5.406A pdb=" N LYS A 454 " --> pdb=" O VAL A 450 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N PHE A 455 " --> pdb=" O ILE A 451 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU A 456 " --> pdb=" O GLY A 452 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ALA A 471 " --> pdb=" O LEU A 467 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N THR A 472 " --> pdb=" O VAL A 468 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N GLN A 475 " --> pdb=" O ALA A 471 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N THR A 476 " --> pdb=" O THR A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 515 Processing helix chain 'A' and resid 524 through 529 Processing helix chain 'A' and resid 574 through 600 Processing helix chain 'A' and resid 605 through 621 Processing helix chain 'A' and resid 634 through 639 Processing helix chain 'A' and resid 641 through 654 removed outlier: 3.822A pdb=" N LYS A 645 " --> pdb=" O TYR A 641 " (cutoff:3.500A) Processing helix chain 'A' and resid 668 through 677 Processing helix chain 'A' and resid 677 through 704 removed outlier: 3.855A pdb=" N GLU A 681 " --> pdb=" O HIS A 677 " (cutoff:3.500A) removed outlier: 3.518A 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 724 through 750 Processing helix chain 'A' and resid 755 through 761 removed outlier: 4.105A pdb=" N ILE A 759 " --> pdb=" O GLY A 755 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N SER A 761 " --> pdb=" O HIS A 757 " (cutoff:3.500A) Processing helix chain 'A' and resid 761 through 783 removed outlier: 3.737A pdb=" N LYS A 765 " --> pdb=" O SER A 761 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N PHE A 766 " --> pdb=" O HIS A 762 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ASP A 767 " --> pdb=" O TRP A 763 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N THR A 783 " --> pdb=" O ILE A 779 " (cutoff:3.500A) Processing helix chain 'A' and resid 799 through 806 removed outlier: 4.546A pdb=" N LEU A 804 " --> pdb=" O LEU A 801 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N LEU A 805 " --> pdb=" O PHE A 802 " (cutoff:3.500A) Processing helix chain 'A' and resid 807 through 812 removed outlier: 4.061A pdb=" N LEU A 811 " --> pdb=" O GLY A 807 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ARG A 812 " --> pdb=" O LEU A 808 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 807 through 812' Processing helix chain 'A' and resid 813 through 857 removed outlier: 3.536A pdb=" N LEU A 817 " --> pdb=" O LEU A 813 " (cutoff:3.500A) Proline residue: A 819 - end of helix removed outlier: 3.512A pdb=" N ARG A 856 " --> pdb=" O LYS A 852 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N MET A 857 " --> pdb=" O ILE A 853 " (cutoff:3.500A) Processing helix chain 'A' and resid 863 through 889 removed outlier: 4.047A pdb=" N ILE A 870 " --> pdb=" O GLU A 866 " (cutoff:3.500A) Processing helix chain 'A' and resid 889 through 919 removed outlier: 3.958A pdb=" N ALA A 893 " --> pdb=" O HIS A 889 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N VAL A 894 " --> pdb=" O PRO A 890 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N SER A 895 " --> pdb=" O GLY A 891 " (cutoff:3.500A) Processing helix chain 'A' and resid 923 through 943 removed outlier: 3.677A pdb=" N ASN A 943 " --> pdb=" O LYS A 939 " (cutoff:3.500A) Processing helix chain 'A' and resid 952 through 959 Processing helix chain 'A' and resid 966 through 976 removed outlier: 3.645A pdb=" N ILE A 970 " --> pdb=" O ASP A 966 " (cutoff:3.500A) Processing helix chain 'A' and resid 1043 through 1050 Processing helix chain 'A' and resid 1069 through 1080 Processing helix chain 'A' and resid 1085 through 1107 removed outlier: 3.698A pdb=" N THR A1100 " --> pdb=" O ILE A1096 " (cutoff:3.500A) Proline residue: A1101 - end of helix Processing helix chain 'A' and resid 1115 through 1123 removed outlier: 3.636A pdb=" N ARG A1123 " --> pdb=" O LEU A1119 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 979 through 982 removed outlier: 3.659A pdb=" N SER B1003 " --> pdb=" O GLN B1064 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N TYR B1066 " --> pdb=" O ILE B1001 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N ILE B1001 " --> pdb=" O TYR B1066 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 987 through 989 removed outlier: 6.877A pdb=" N VAL B 987 " --> pdb=" O CYS B1059 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N CYS B1059 " --> pdb=" O VAL B 987 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N VAL B 989 " --> pdb=" O VAL B1057 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N VAL B1057 " --> pdb=" O VAL B 989 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 1125 through 1126 removed outlier: 6.819A pdb=" N ARG B1185 " --> pdb=" O ILE B1148 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 1153 through 1154 removed outlier: 3.937A pdb=" N TYR B1153 " --> pdb=" O THR B1175 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 979 through 982 removed outlier: 3.652A pdb=" N SER A1003 " --> pdb=" O GLN A1064 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N TYR A1066 " --> pdb=" O ILE A1001 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N ILE A1001 " --> pdb=" O TYR A1066 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 987 through 989 removed outlier: 6.880A pdb=" N VAL A 987 " --> pdb=" O CYS A1059 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N CYS A1059 " --> pdb=" O VAL A 987 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N VAL A 989 " --> pdb=" O VAL A1057 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N VAL A1057 " --> pdb=" O VAL A 989 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1125 through 1126 removed outlier: 6.747A pdb=" N ARG A1185 " --> pdb=" O ILE A1148 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1153 through 1154 removed outlier: 3.914A pdb=" N TYR A1153 " --> pdb=" O THR A1175 " (cutoff:3.500A) 1119 hydrogen bonds defined for protein. 3309 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.78 Time building geometry restraints manager: 1.75 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: 2812 1.33 - 1.45: 3843 1.45 - 1.57: 9448 1.57 - 1.69: 1 1.69 - 1.81: 140 Bond restraints: 16244 Sorted by residual: bond pdb=" N PRO A1184 " pdb=" CD PRO A1184 " ideal model delta sigma weight residual 1.473 1.537 -0.064 1.40e-02 5.10e+03 2.11e+01 bond pdb=" N PRO A1184 " pdb=" CA PRO A1184 " ideal model delta sigma weight residual 1.470 1.421 0.050 1.23e-02 6.61e+03 1.62e+01 bond pdb=" CB PRO A1184 " pdb=" CG PRO A1184 " ideal model delta sigma weight residual 1.492 1.688 -0.196 5.00e-02 4.00e+02 1.54e+01 bond pdb=" CG PRO A1184 " pdb=" CD PRO A1184 " ideal model delta sigma weight residual 1.503 1.371 0.132 3.40e-02 8.65e+02 1.50e+01 bond pdb=" N GLY A 836 " pdb=" CA GLY A 836 " ideal model delta sigma weight residual 1.454 1.444 0.010 1.22e-02 6.72e+03 6.79e-01 ... (remaining 16239 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.14: 22045 4.14 - 8.28: 6 8.28 - 12.43: 2 12.43 - 16.57: 0 16.57 - 20.71: 1 Bond angle restraints: 22054 Sorted by residual: angle pdb=" CA PRO A1184 " pdb=" N PRO A1184 " pdb=" CD PRO A1184 " ideal model delta sigma weight residual 112.00 91.29 20.71 1.40e+00 5.10e-01 2.19e+02 angle pdb=" N PRO A1184 " pdb=" CD PRO A1184 " pdb=" CG PRO A1184 " ideal model delta sigma weight residual 103.20 93.22 9.98 1.50e+00 4.44e-01 4.42e+01 angle pdb=" CA PRO A1184 " pdb=" CB PRO A1184 " pdb=" CG PRO A1184 " ideal model delta sigma weight residual 104.50 95.15 9.35 1.90e+00 2.77e-01 2.42e+01 angle pdb=" N PRO A1184 " pdb=" CA PRO A1184 " pdb=" CB PRO A1184 " ideal model delta sigma weight residual 103.36 100.30 3.06 8.30e-01 1.45e+00 1.36e+01 angle pdb=" N PRO A1184 " pdb=" CA PRO A1184 " pdb=" C PRO A1184 " ideal model delta sigma weight residual 110.55 116.16 -5.61 1.63e+00 3.76e-01 1.19e+01 ... (remaining 22049 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.36: 8247 17.36 - 34.71: 1072 34.71 - 52.07: 302 52.07 - 69.43: 70 69.43 - 86.78: 19 Dihedral angle restraints: 9710 sinusoidal: 3576 harmonic: 6134 Sorted by residual: dihedral pdb=" CA VAL B1171 " pdb=" C VAL B1171 " pdb=" N HIS B1172 " pdb=" CA HIS B1172 " ideal model delta harmonic sigma weight residual 180.00 -162.01 -17.99 0 5.00e+00 4.00e-02 1.30e+01 dihedral pdb=" CA ASP B 68 " pdb=" CB ASP B 68 " pdb=" CG ASP B 68 " pdb=" OD1 ASP B 68 " ideal model delta sinusoidal sigma weight residual -30.00 -88.60 58.60 1 2.00e+01 2.50e-03 1.15e+01 dihedral pdb=" CB GLU B1131 " pdb=" CG GLU B1131 " pdb=" CD GLU B1131 " pdb=" OE1 GLU B1131 " ideal model delta sinusoidal sigma weight residual 0.00 -86.78 86.78 1 3.00e+01 1.11e-03 1.01e+01 ... (remaining 9707 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 2235 0.052 - 0.104: 400 0.104 - 0.156: 22 0.156 - 0.208: 0 0.208 - 0.259: 1 Chirality restraints: 2658 Sorted by residual: chirality pdb=" CA PRO A1184 " pdb=" N PRO A1184 " pdb=" C PRO A1184 " pdb=" CB PRO A1184 " both_signs ideal model delta sigma weight residual False 2.72 2.46 0.26 2.00e-01 2.50e+01 1.68e+00 chirality pdb=" CA VAL B 321 " pdb=" N VAL B 321 " pdb=" C VAL B 321 " pdb=" CB VAL B 321 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.41e-01 chirality pdb=" CA VAL A 321 " pdb=" N VAL A 321 " pdb=" C VAL A 321 " pdb=" CB VAL A 321 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.39e-01 ... (remaining 2655 not shown) Planarity restraints: 2754 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A1183 " -0.115 5.00e-02 4.00e+02 1.54e-01 3.77e+01 pdb=" N PRO A1184 " 0.264 5.00e-02 4.00e+02 pdb=" CA PRO A1184 " -0.071 5.00e-02 4.00e+02 pdb=" CD PRO A1184 " -0.078 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR A 641 " -0.040 5.00e-02 4.00e+02 6.10e-02 5.95e+00 pdb=" N PRO A 642 " 0.105 5.00e-02 4.00e+02 pdb=" CA PRO A 642 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 642 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR B 641 " 0.027 5.00e-02 4.00e+02 4.13e-02 2.73e+00 pdb=" N PRO B 642 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO B 642 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 642 " 0.023 5.00e-02 4.00e+02 ... (remaining 2751 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 202 2.63 - 3.19: 16452 3.19 - 3.76: 24747 3.76 - 4.33: 30964 4.33 - 4.90: 52442 Nonbonded interactions: 124807 Sorted by model distance: nonbonded pdb=" OD1 ASP B1139 " pdb=" OG1 THR B1141 " model vdw 2.057 3.040 nonbonded pdb=" N GLU B 924 " pdb=" OE1 GLU B 924 " model vdw 2.083 3.120 nonbonded pdb=" OE1 GLU A 590 " pdb=" OH TYR A 594 " model vdw 2.104 3.040 nonbonded pdb=" OE1 GLU B 590 " pdb=" OH TYR B 594 " model vdw 2.106 3.040 nonbonded pdb=" O PRO A 952 " pdb=" ND2 ASN A 955 " model vdw 2.134 3.120 ... (remaining 124802 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.03 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 68 through 131 or resid 133 through 1402)) selection = (chain 'B' and (resid 68 through 131 or resid 133 through 1402)) } 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=0.36 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: 5.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 16.660 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.196 16244 Z= 0.123 Angle : 0.444 20.712 22054 Z= 0.258 Chirality : 0.035 0.259 2658 Planarity : 0.004 0.154 2754 Dihedral : 17.407 86.784 5730 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 35.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 0.00 % Allowed : 34.19 % Favored : 65.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.35 (0.20), residues: 2094 helix: 2.80 (0.14), residues: 1426 sheet: -0.01 (0.56), residues: 76 loop : -1.50 (0.27), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1185 TYR 0.008 0.001 TYR B 309 PHE 0.011 0.001 PHE A1134 TRP 0.013 0.001 TRP B 278 HIS 0.007 0.001 HIS B1172 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.12 (16244) covalent geometry : angle 0.44362 / 0.26 (22054) hydrogen bonds : bond 0.12681 / 8.13 ( 1119) hydrogen bonds : angle 5.43732 / 4.15 ( 3309) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 134 time to evaluate : 0.469 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 134 average time/residue: 0.0942 time to fit residues: 20.3850 Evaluate side-chains 129 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 129 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 6.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.0370 chunk 103 optimal weight: 10.0000 chunk 200 optimal weight: 0.9980 chunk 77 optimal weight: 0.5980 chunk 122 optimal weight: 0.7980 overall best weight: 0.8860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 614 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN ** B1154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 614 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN ** A1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1154 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.115296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.074594 restraints weight = 51677.060| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 3.44 r_work: 0.3007 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3004 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3004 r_free = 0.3004 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3004 r_free = 0.3004 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3004 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.1060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.089 16244 Z= 0.152 Angle : 0.610 11.042 22054 Z= 0.311 Chirality : 0.040 0.184 2658 Planarity : 0.004 0.074 2754 Dihedral : 7.222 59.174 2368 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.59 % Favored : 95.36 % Rotamer: Outliers : 2.05 % Allowed : 31.88 % Favored : 66.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.21 (0.19), residues: 2094 helix: 2.68 (0.14), residues: 1422 sheet: 0.84 (0.68), residues: 58 loop : -1.58 (0.26), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 856 TYR 0.011 0.001 TYR B1153 PHE 0.012 0.001 PHE B1134 TRP 0.010 0.001 TRP A 962 HIS 0.009 0.001 HIS A1172 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.15 (16244) covalent geometry : angle 0.60953 / 0.31 (22054) hydrogen bonds : bond 0.05127 / 3.42 ( 1119) hydrogen bonds : angle 4.27457 / 3.22 ( 3309) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 153 time to evaluate : 0.512 Fit side-chains REVERT: B 483 MET cc_start: 0.8866 (mtp) cc_final: 0.8656 (mtp) REVERT: B 532 ILE cc_start: 0.9331 (mm) cc_final: 0.9093 (mp) REVERT: B 609 ARG cc_start: 0.9355 (tpt90) cc_final: 0.9049 (tmm-80) REVERT: B 943 ASN cc_start: 0.8805 (t0) cc_final: 0.8344 (p0) REVERT: B 967 MET cc_start: 0.8265 (mmm) cc_final: 0.7958 (tmm) REVERT: B 1066 TYR cc_start: 0.8694 (OUTLIER) cc_final: 0.7884 (m-80) REVERT: B 1107 MET cc_start: 0.7558 (tmm) cc_final: 0.7305 (tmm) REVERT: A 532 ILE cc_start: 0.9330 (mm) cc_final: 0.9100 (mp) REVERT: A 849 GLU cc_start: 0.8916 (OUTLIER) cc_final: 0.8576 (mp0) REVERT: A 967 MET cc_start: 0.8299 (mmm) cc_final: 0.8020 (tmm) REVERT: A 1107 MET cc_start: 0.7528 (tmm) cc_final: 0.7290 (tmm) outliers start: 32 outliers final: 10 residues processed: 182 average time/residue: 0.1140 time to fit residues: 31.4806 Evaluate side-chains 150 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 138 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 398 ILE Chi-restraints excluded: chain B residue 895 SER Chi-restraints excluded: chain B residue 1056 THR Chi-restraints excluded: chain B residue 1066 TYR Chi-restraints excluded: chain B residue 1127 VAL Chi-restraints excluded: chain B residue 1181 THR Chi-restraints excluded: chain A residue 398 ILE Chi-restraints excluded: chain A residue 595 TRP Chi-restraints excluded: chain A residue 849 GLU Chi-restraints excluded: chain A residue 857 MET Chi-restraints excluded: chain A residue 1127 VAL Chi-restraints excluded: chain A residue 1181 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 113 optimal weight: 2.9990 chunk 146 optimal weight: 0.9990 chunk 164 optimal weight: 50.0000 chunk 178 optimal weight: 2.9990 chunk 82 optimal weight: 0.9980 chunk 136 optimal weight: 5.9990 chunk 135 optimal weight: 0.8980 chunk 190 optimal weight: 7.9990 chunk 26 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 143 optimal weight: 2.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 614 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 614 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.113772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.072077 restraints weight = 72159.169| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 4.00 r_work: 0.2950 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2945 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2945 r_free = 0.2945 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2945 r_free = 0.2945 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2945 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.1256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 16244 Z= 0.186 Angle : 0.610 13.031 22054 Z= 0.311 Chirality : 0.040 0.179 2658 Planarity : 0.004 0.077 2754 Dihedral : 7.428 58.313 2368 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.73 % Favored : 95.22 % Rotamer: Outliers : 2.43 % Allowed : 30.99 % Favored : 66.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.97 (0.19), residues: 2094 helix: 2.54 (0.13), residues: 1436 sheet: -0.86 (0.60), residues: 82 loop : -1.71 (0.26), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 609 TYR 0.018 0.001 TYR B 641 PHE 0.025 0.001 PHE B 598 TRP 0.013 0.002 TRP B 962 HIS 0.010 0.001 HIS A1172 Details of bonding type rmsd/Z covalent geometry : bond 0.00440 / 0.19 (16244) covalent geometry : angle 0.61005 / 0.31 (22054) hydrogen bonds : bond 0.05430 / 3.63 ( 1119) hydrogen bonds : angle 4.22106 / 3.18 ( 3309) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 144 time to evaluate : 0.578 Fit side-chains REVERT: B 483 MET cc_start: 0.8920 (mtp) cc_final: 0.8667 (mtp) REVERT: B 512 LEU cc_start: 0.9576 (OUTLIER) cc_final: 0.9120 (mm) REVERT: B 532 ILE cc_start: 0.9354 (OUTLIER) cc_final: 0.9095 (mp) REVERT: B 609 ARG cc_start: 0.9368 (tpt90) cc_final: 0.9029 (tmm-80) REVERT: B 837 TYR cc_start: 0.8618 (OUTLIER) cc_final: 0.7480 (m-80) REVERT: B 849 GLU cc_start: 0.9076 (OUTLIER) cc_final: 0.8552 (mp0) REVERT: B 1066 TYR cc_start: 0.8784 (OUTLIER) cc_final: 0.7935 (m-80) REVERT: B 1073 MET cc_start: 0.8687 (mmm) cc_final: 0.8475 (mmt) REVERT: B 1107 MET cc_start: 0.7531 (tmm) cc_final: 0.7233 (tmm) REVERT: B 1166 LEU cc_start: 0.7274 (OUTLIER) cc_final: 0.7074 (tt) REVERT: A 129 ASP cc_start: 0.8311 (OUTLIER) cc_final: 0.8054 (t0) REVERT: A 532 ILE cc_start: 0.9343 (OUTLIER) cc_final: 0.9048 (mp) REVERT: A 609 ARG cc_start: 0.9213 (tpt90) cc_final: 0.8916 (ptm160) REVERT: A 849 GLU cc_start: 0.8972 (OUTLIER) cc_final: 0.8569 (mp0) REVERT: A 1073 MET cc_start: 0.8678 (mmm) cc_final: 0.8469 (mmt) outliers start: 38 outliers final: 15 residues processed: 174 average time/residue: 0.1093 time to fit residues: 29.1277 Evaluate side-chains 159 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 135 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 191 TYR Chi-restraints excluded: chain B residue 448 ASN Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 532 ILE Chi-restraints excluded: chain B residue 837 TYR Chi-restraints excluded: chain B residue 849 GLU Chi-restraints excluded: chain B residue 895 SER Chi-restraints excluded: chain B residue 1056 THR Chi-restraints excluded: chain B residue 1066 TYR Chi-restraints excluded: chain B residue 1166 LEU Chi-restraints excluded: chain B residue 1181 THR Chi-restraints excluded: chain A residue 129 ASP Chi-restraints excluded: chain A residue 191 TYR Chi-restraints excluded: chain A residue 398 ILE Chi-restraints excluded: chain A residue 448 ASN Chi-restraints excluded: chain A residue 532 ILE Chi-restraints excluded: chain A residue 575 PHE Chi-restraints excluded: chain A residue 595 TRP Chi-restraints excluded: chain A residue 635 TRP Chi-restraints excluded: chain A residue 849 GLU Chi-restraints excluded: chain A residue 867 LEU Chi-restraints excluded: chain A residue 915 GLU Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain A residue 1181 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 85 optimal weight: 0.0040 chunk 165 optimal weight: 30.0000 chunk 153 optimal weight: 9.9990 chunk 37 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 chunk 38 optimal weight: 0.5980 chunk 73 optimal weight: 5.9990 chunk 6 optimal weight: 8.9990 chunk 68 optimal weight: 10.0000 chunk 191 optimal weight: 3.9990 chunk 136 optimal weight: 4.9990 overall best weight: 1.7196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 614 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1156 HIS ** A 614 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.113061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.071399 restraints weight = 60865.670| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 3.62 r_work: 0.2938 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2940 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2940 r_free = 0.2940 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2940 r_free = 0.2940 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2940 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.1417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 16244 Z= 0.178 Angle : 0.599 11.047 22054 Z= 0.306 Chirality : 0.040 0.162 2658 Planarity : 0.004 0.080 2754 Dihedral : 7.422 58.093 2368 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 3.71 % Allowed : 30.35 % Favored : 65.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.90 (0.19), residues: 2094 helix: 2.53 (0.13), residues: 1428 sheet: -0.87 (0.60), residues: 82 loop : -1.82 (0.25), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 609 TYR 0.018 0.001 TYR B 641 PHE 0.020 0.001 PHE B 972 TRP 0.014 0.002 TRP B 635 HIS 0.007 0.001 HIS A1172 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.18 (16244) covalent geometry : angle 0.59864 / 0.31 (22054) hydrogen bonds : bond 0.05374 / 3.61 ( 1119) hydrogen bonds : angle 4.13020 / 3.11 ( 3309) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 141 time to evaluate : 0.586 Fit side-chains REVERT: B 483 MET cc_start: 0.9000 (mtp) cc_final: 0.8737 (mtp) REVERT: B 512 LEU cc_start: 0.9601 (OUTLIER) cc_final: 0.9138 (mm) REVERT: B 609 ARG cc_start: 0.9339 (tpt90) cc_final: 0.9005 (tmm-80) REVERT: B 837 TYR cc_start: 0.8677 (OUTLIER) cc_final: 0.7561 (m-80) REVERT: B 849 GLU cc_start: 0.9011 (OUTLIER) cc_final: 0.8464 (mp0) REVERT: B 967 MET cc_start: 0.8630 (tpp) cc_final: 0.8337 (tmm) REVERT: A 129 ASP cc_start: 0.8307 (OUTLIER) cc_final: 0.8052 (t0) REVERT: A 512 LEU cc_start: 0.9602 (OUTLIER) cc_final: 0.9153 (mm) REVERT: A 532 ILE cc_start: 0.9326 (OUTLIER) cc_final: 0.9053 (mp) REVERT: A 609 ARG cc_start: 0.9168 (tpt90) cc_final: 0.8882 (ptm160) REVERT: A 849 GLU cc_start: 0.8880 (OUTLIER) cc_final: 0.8514 (mp0) REVERT: A 967 MET cc_start: 0.8607 (tpp) cc_final: 0.8314 (tmm) REVERT: A 1107 MET cc_start: 0.7493 (tmm) cc_final: 0.7287 (tmm) outliers start: 58 outliers final: 26 residues processed: 190 average time/residue: 0.1064 time to fit residues: 31.5860 Evaluate side-chains 171 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 138 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 191 TYR Chi-restraints excluded: chain B residue 398 ILE Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain B residue 448 ASN Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 837 TYR Chi-restraints excluded: chain B residue 849 GLU Chi-restraints excluded: chain B residue 895 SER Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1000 LEU Chi-restraints excluded: chain B residue 1002 VAL Chi-restraints excluded: chain B residue 1056 THR Chi-restraints excluded: chain B residue 1181 THR Chi-restraints excluded: chain A residue 129 ASP Chi-restraints excluded: chain A residue 191 TYR Chi-restraints excluded: chain A residue 398 ILE Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 448 ASN Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 532 ILE Chi-restraints excluded: chain A residue 575 PHE Chi-restraints excluded: chain A residue 595 TRP Chi-restraints excluded: chain A residue 635 TRP Chi-restraints excluded: chain A residue 822 ILE Chi-restraints excluded: chain A residue 849 GLU Chi-restraints excluded: chain A residue 895 SER Chi-restraints excluded: chain A residue 915 GLU Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 1002 VAL Chi-restraints excluded: chain A residue 1127 VAL Chi-restraints excluded: chain A residue 1181 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 5 optimal weight: 3.9990 chunk 192 optimal weight: 6.9990 chunk 131 optimal weight: 1.9990 chunk 198 optimal weight: 1.9990 chunk 127 optimal weight: 1.9990 chunk 15 optimal weight: 5.9990 chunk 174 optimal weight: 0.2980 chunk 43 optimal weight: 4.9990 chunk 103 optimal weight: 5.9990 chunk 179 optimal weight: 5.9990 chunk 77 optimal weight: 3.9990 overall best weight: 2.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 614 HIS ** B1154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 614 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.112451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.071264 restraints weight = 52469.541| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 3.36 r_work: 0.2940 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2942 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2942 r_free = 0.2942 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2942 r_free = 0.2942 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2942 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.1588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 16244 Z= 0.203 Angle : 0.614 12.047 22054 Z= 0.314 Chirality : 0.040 0.169 2658 Planarity : 0.004 0.078 2754 Dihedral : 7.568 58.864 2368 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 3.46 % Allowed : 30.22 % Favored : 66.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.83 (0.19), residues: 2094 helix: 2.49 (0.13), residues: 1422 sheet: -0.96 (0.59), residues: 82 loop : -1.82 (0.25), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 609 TYR 0.017 0.001 TYR B 641 PHE 0.033 0.001 PHE B 598 TRP 0.017 0.002 TRP B 635 HIS 0.006 0.001 HIS A1172 Details of bonding type rmsd/Z covalent geometry : bond 0.00485 / 0.20 (16244) covalent geometry : angle 0.61367 / 0.31 (22054) hydrogen bonds : bond 0.05613 / 3.77 ( 1119) hydrogen bonds : angle 4.16126 / 3.12 ( 3309) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 137 time to evaluate : 0.621 Fit side-chains REVERT: B 512 LEU cc_start: 0.9607 (OUTLIER) cc_final: 0.9111 (mm) REVERT: B 602 MET cc_start: 0.6027 (mmp) cc_final: 0.5770 (mmp) REVERT: B 609 ARG cc_start: 0.9318 (tpt90) cc_final: 0.9000 (tmm-80) REVERT: B 837 TYR cc_start: 0.8766 (OUTLIER) cc_final: 0.7813 (m-80) REVERT: B 849 GLU cc_start: 0.8998 (OUTLIER) cc_final: 0.8499 (mp0) REVERT: B 935 GLU cc_start: 0.8846 (tp30) cc_final: 0.8632 (tp30) REVERT: B 967 MET cc_start: 0.8608 (tpp) cc_final: 0.8235 (tmm) REVERT: B 1107 MET cc_start: 0.7459 (tmm) cc_final: 0.7242 (tmm) REVERT: B 1139 ASP cc_start: 0.6752 (OUTLIER) cc_final: 0.6466 (p0) REVERT: A 129 ASP cc_start: 0.8280 (OUTLIER) cc_final: 0.8021 (t0) REVERT: A 220 LEU cc_start: 0.8416 (OUTLIER) cc_final: 0.7903 (mp) REVERT: A 512 LEU cc_start: 0.9605 (OUTLIER) cc_final: 0.9110 (mm) REVERT: A 849 GLU cc_start: 0.8854 (OUTLIER) cc_final: 0.8482 (mp0) REVERT: A 967 MET cc_start: 0.8610 (tpp) cc_final: 0.8241 (tmm) outliers start: 54 outliers final: 30 residues processed: 184 average time/residue: 0.0933 time to fit residues: 27.3341 Evaluate side-chains 172 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 134 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 191 TYR Chi-restraints excluded: chain B residue 398 ILE Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain B residue 448 ASN Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 575 PHE Chi-restraints excluded: chain B residue 837 TYR Chi-restraints excluded: chain B residue 849 GLU Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 979 LEU Chi-restraints excluded: chain B residue 1000 LEU Chi-restraints excluded: chain B residue 1002 VAL Chi-restraints excluded: chain B residue 1056 THR Chi-restraints excluded: chain B residue 1062 THR Chi-restraints excluded: chain B residue 1127 VAL Chi-restraints excluded: chain B residue 1139 ASP Chi-restraints excluded: chain B residue 1181 THR Chi-restraints excluded: chain A residue 129 ASP Chi-restraints excluded: chain A residue 191 TYR Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 448 ASN Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 575 PHE Chi-restraints excluded: chain A residue 595 TRP Chi-restraints excluded: chain A residue 635 TRP Chi-restraints excluded: chain A residue 849 GLU Chi-restraints excluded: chain A residue 867 LEU Chi-restraints excluded: chain A residue 895 SER Chi-restraints excluded: chain A residue 915 GLU Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 979 LEU Chi-restraints excluded: chain A residue 1002 VAL Chi-restraints excluded: chain A residue 1062 THR Chi-restraints excluded: chain A residue 1127 VAL Chi-restraints excluded: chain A residue 1181 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 39 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 chunk 120 optimal weight: 0.7980 chunk 77 optimal weight: 4.9990 chunk 124 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 chunk 178 optimal weight: 9.9990 chunk 141 optimal weight: 3.9990 chunk 122 optimal weight: 0.9990 chunk 206 optimal weight: 6.9990 chunk 135 optimal weight: 0.6980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B1154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 614 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1149 ASN ** A1172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.114803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.073432 restraints weight = 61230.820| |-----------------------------------------------------------------------------| r_work (start): 0.3130 rms_B_bonded: 3.63 r_work: 0.2979 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2975 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2975 r_free = 0.2975 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2975 r_free = 0.2975 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2975 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.1747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 16244 Z= 0.125 Angle : 0.554 10.483 22054 Z= 0.281 Chirality : 0.038 0.156 2658 Planarity : 0.004 0.077 2754 Dihedral : 7.398 58.954 2368 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 2.88 % Allowed : 30.60 % Favored : 66.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.04 (0.19), residues: 2094 helix: 2.67 (0.14), residues: 1414 sheet: -0.87 (0.60), residues: 82 loop : -1.74 (0.25), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 976 TYR 0.016 0.001 TYR B 641 PHE 0.022 0.001 PHE B 598 TRP 0.014 0.001 TRP B 635 HIS 0.006 0.001 HIS A1172 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 (16244) covalent geometry : angle 0.55438 / 0.28 (22054) hydrogen bonds : bond 0.04624 / 3.10 ( 1119) hydrogen bonds : angle 3.95896 / 2.97 ( 3309) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 142 time to evaluate : 0.612 Fit side-chains REVERT: B 483 MET cc_start: 0.9040 (OUTLIER) cc_final: 0.8811 (mtp) REVERT: B 512 LEU cc_start: 0.9563 (OUTLIER) cc_final: 0.9083 (mm) REVERT: B 532 ILE cc_start: 0.9316 (OUTLIER) cc_final: 0.9097 (mp) REVERT: B 609 ARG cc_start: 0.9293 (tpt90) cc_final: 0.8973 (tmm-80) REVERT: B 837 TYR cc_start: 0.8814 (OUTLIER) cc_final: 0.7713 (m-80) REVERT: B 849 GLU cc_start: 0.8926 (OUTLIER) cc_final: 0.8368 (mp0) REVERT: B 914 HIS cc_start: 0.8820 (OUTLIER) cc_final: 0.8514 (m170) REVERT: B 924 GLU cc_start: 0.7828 (mp0) cc_final: 0.6919 (mp0) REVERT: B 935 GLU cc_start: 0.8853 (tp30) cc_final: 0.8619 (tp30) REVERT: B 967 MET cc_start: 0.8664 (tpp) cc_final: 0.8293 (tmm) REVERT: B 1107 MET cc_start: 0.7416 (tmm) cc_final: 0.7189 (tmm) REVERT: B 1139 ASP cc_start: 0.6617 (OUTLIER) cc_final: 0.6351 (p0) REVERT: A 129 ASP cc_start: 0.8223 (OUTLIER) cc_final: 0.7963 (t0) REVERT: A 220 LEU cc_start: 0.8348 (OUTLIER) cc_final: 0.7832 (mp) REVERT: A 512 LEU cc_start: 0.9566 (OUTLIER) cc_final: 0.9093 (mm) REVERT: A 595 TRP cc_start: 0.8610 (OUTLIER) cc_final: 0.7789 (m100) REVERT: A 602 MET cc_start: 0.6147 (mmp) cc_final: 0.5698 (mmp) REVERT: A 849 GLU cc_start: 0.8771 (OUTLIER) cc_final: 0.8383 (mp0) REVERT: A 967 MET cc_start: 0.8689 (tpp) cc_final: 0.8319 (tmm) REVERT: A 1009 TYR cc_start: 0.8266 (t80) cc_final: 0.7976 (t80) outliers start: 45 outliers final: 22 residues processed: 180 average time/residue: 0.1046 time to fit residues: 29.3693 Evaluate side-chains 175 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 141 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 224 LYS Chi-restraints excluded: chain B residue 398 ILE Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain B residue 483 MET Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 532 ILE Chi-restraints excluded: chain B residue 575 PHE Chi-restraints excluded: chain B residue 837 TYR Chi-restraints excluded: chain B residue 849 GLU Chi-restraints excluded: chain B residue 914 HIS Chi-restraints excluded: chain B residue 979 LEU Chi-restraints excluded: chain B residue 1056 THR Chi-restraints excluded: chain B residue 1062 THR Chi-restraints excluded: chain B residue 1127 VAL Chi-restraints excluded: chain B residue 1139 ASP Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 129 ASP Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 398 ILE Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 575 PHE Chi-restraints excluded: chain A residue 595 TRP Chi-restraints excluded: chain A residue 849 GLU Chi-restraints excluded: chain A residue 895 SER Chi-restraints excluded: chain A residue 915 GLU Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain A residue 979 LEU Chi-restraints excluded: chain A residue 1005 LEU Chi-restraints excluded: chain A residue 1062 THR Chi-restraints excluded: chain A residue 1127 VAL Chi-restraints excluded: chain A residue 1181 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 143 optimal weight: 0.3980 chunk 90 optimal weight: 1.9990 chunk 44 optimal weight: 5.9990 chunk 173 optimal weight: 40.0000 chunk 144 optimal weight: 0.9980 chunk 66 optimal weight: 4.9990 chunk 154 optimal weight: 0.8980 chunk 116 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 117 optimal weight: 0.8980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B1154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 614 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.114586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.073725 restraints weight = 47279.759| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 3.18 r_work: 0.2995 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2995 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2995 r_free = 0.2995 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2995 r_free = 0.2995 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2995 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.1798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 16244 Z= 0.134 Angle : 0.569 15.510 22054 Z= 0.287 Chirality : 0.039 0.185 2658 Planarity : 0.004 0.075 2754 Dihedral : 7.385 59.114 2368 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 2.82 % Allowed : 30.41 % Favored : 66.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.04 (0.19), residues: 2094 helix: 2.65 (0.14), residues: 1420 sheet: -0.82 (0.59), residues: 82 loop : -1.74 (0.25), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 976 TYR 0.014 0.001 TYR B 641 PHE 0.034 0.001 PHE B 598 TRP 0.020 0.002 TRP B 643 HIS 0.005 0.001 HIS A1172 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.13 (16244) covalent geometry : angle 0.56928 / 0.29 (22054) hydrogen bonds : bond 0.04683 / 3.14 ( 1119) hydrogen bonds : angle 3.95305 / 2.96 ( 3309) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 144 time to evaluate : 0.462 Fit side-chains REVERT: B 483 MET cc_start: 0.9017 (mtp) cc_final: 0.8797 (mtp) REVERT: B 512 LEU cc_start: 0.9568 (OUTLIER) cc_final: 0.9090 (mm) REVERT: B 609 ARG cc_start: 0.9247 (tpt90) cc_final: 0.8940 (tmm-80) REVERT: B 837 TYR cc_start: 0.8798 (OUTLIER) cc_final: 0.7701 (m-80) REVERT: B 849 GLU cc_start: 0.8932 (OUTLIER) cc_final: 0.8374 (mp0) REVERT: B 924 GLU cc_start: 0.7871 (mp0) cc_final: 0.7211 (mp0) REVERT: B 935 GLU cc_start: 0.8805 (tp30) cc_final: 0.8563 (tp30) REVERT: B 967 MET cc_start: 0.8675 (tpp) cc_final: 0.8275 (tmm) REVERT: B 1107 MET cc_start: 0.7365 (tmm) cc_final: 0.7118 (tmm) REVERT: B 1139 ASP cc_start: 0.6747 (OUTLIER) cc_final: 0.6139 (p0) REVERT: A 129 ASP cc_start: 0.8247 (OUTLIER) cc_final: 0.7989 (t0) REVERT: A 220 LEU cc_start: 0.8341 (OUTLIER) cc_final: 0.7819 (mp) REVERT: A 512 LEU cc_start: 0.9567 (OUTLIER) cc_final: 0.9085 (mm) REVERT: A 595 TRP cc_start: 0.8589 (OUTLIER) cc_final: 0.7850 (m100) REVERT: A 602 MET cc_start: 0.6061 (mmp) cc_final: 0.5664 (mmp) REVERT: A 849 GLU cc_start: 0.8791 (OUTLIER) cc_final: 0.8389 (mp0) REVERT: A 1009 TYR cc_start: 0.8271 (t80) cc_final: 0.7932 (t80) outliers start: 44 outliers final: 26 residues processed: 181 average time/residue: 0.0992 time to fit residues: 27.5508 Evaluate side-chains 174 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 139 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 398 ILE Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 635 TRP Chi-restraints excluded: chain B residue 837 TYR Chi-restraints excluded: chain B residue 849 GLU Chi-restraints excluded: chain B residue 932 LEU Chi-restraints excluded: chain B residue 979 LEU Chi-restraints excluded: chain B residue 1002 VAL Chi-restraints excluded: chain B residue 1005 LEU Chi-restraints excluded: chain B residue 1056 THR Chi-restraints excluded: chain B residue 1062 THR Chi-restraints excluded: chain B residue 1127 VAL Chi-restraints excluded: chain B residue 1139 ASP Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 129 ASP Chi-restraints excluded: chain A residue 136 HIS Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 224 LYS Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 398 ILE Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 575 PHE Chi-restraints excluded: chain A residue 595 TRP Chi-restraints excluded: chain A residue 635 TRP Chi-restraints excluded: chain A residue 849 GLU Chi-restraints excluded: chain A residue 915 GLU Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain A residue 979 LEU Chi-restraints excluded: chain A residue 1002 VAL Chi-restraints excluded: chain A residue 1005 LEU Chi-restraints excluded: chain A residue 1062 THR Chi-restraints excluded: chain A residue 1127 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 16 optimal weight: 3.9990 chunk 5 optimal weight: 0.0770 chunk 73 optimal weight: 3.9990 chunk 180 optimal weight: 0.5980 chunk 63 optimal weight: 50.0000 chunk 33 optimal weight: 3.9990 chunk 74 optimal weight: 3.9990 chunk 186 optimal weight: 0.7980 chunk 10 optimal weight: 0.9990 chunk 110 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 overall best weight: 0.8942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B1154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 614 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1135 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.115127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.073629 restraints weight = 60081.405| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 3.60 r_work: 0.2988 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2983 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2983 r_free = 0.2983 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2983 r_free = 0.2983 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2983 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.1886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 16244 Z= 0.127 Angle : 0.577 15.277 22054 Z= 0.289 Chirality : 0.039 0.226 2658 Planarity : 0.004 0.080 2754 Dihedral : 7.354 59.574 2368 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.40 % Favored : 95.51 % Rotamer: Outliers : 2.69 % Allowed : 30.73 % Favored : 66.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.06 (0.19), residues: 2094 helix: 2.65 (0.14), residues: 1422 sheet: -0.75 (0.60), residues: 82 loop : -1.73 (0.25), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 609 TYR 0.013 0.001 TYR A 641 PHE 0.027 0.001 PHE B 598 TRP 0.016 0.001 TRP A 635 HIS 0.005 0.001 HIS A1172 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.13 (16244) covalent geometry : angle 0.57735 / 0.29 (22054) hydrogen bonds : bond 0.04510 / 3.03 ( 1119) hydrogen bonds : angle 3.90109 / 2.92 ( 3309) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 140 time to evaluate : 0.428 Fit side-chains REVERT: B 483 MET cc_start: 0.9060 (mtp) cc_final: 0.8845 (mtp) REVERT: B 532 ILE cc_start: 0.9318 (OUTLIER) cc_final: 0.9087 (mp) REVERT: B 837 TYR cc_start: 0.8792 (OUTLIER) cc_final: 0.7612 (m-80) REVERT: B 849 GLU cc_start: 0.8934 (OUTLIER) cc_final: 0.8368 (mp0) REVERT: B 914 HIS cc_start: 0.8798 (OUTLIER) cc_final: 0.8490 (m170) REVERT: B 924 GLU cc_start: 0.7847 (mp0) cc_final: 0.7167 (mp0) REVERT: B 935 GLU cc_start: 0.8827 (tp30) cc_final: 0.8580 (tp30) REVERT: B 1139 ASP cc_start: 0.6574 (OUTLIER) cc_final: 0.5980 (p0) REVERT: A 129 ASP cc_start: 0.8230 (OUTLIER) cc_final: 0.7965 (t0) REVERT: A 220 LEU cc_start: 0.8284 (OUTLIER) cc_final: 0.7767 (mp) REVERT: A 595 TRP cc_start: 0.8608 (OUTLIER) cc_final: 0.7841 (m100) REVERT: A 602 MET cc_start: 0.6056 (mmp) cc_final: 0.5708 (mmp) REVERT: A 609 ARG cc_start: 0.9112 (tpt90) cc_final: 0.8906 (ptm160) REVERT: A 849 GLU cc_start: 0.8755 (OUTLIER) cc_final: 0.8300 (mp0) REVERT: A 967 MET cc_start: 0.8761 (tpp) cc_final: 0.8351 (tmm) REVERT: A 1009 TYR cc_start: 0.8315 (t80) cc_final: 0.7949 (t80) outliers start: 42 outliers final: 27 residues processed: 179 average time/residue: 0.1030 time to fit residues: 28.8344 Evaluate side-chains 174 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 138 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 191 TYR Chi-restraints excluded: chain B residue 398 ILE Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain B residue 532 ILE Chi-restraints excluded: chain B residue 635 TRP Chi-restraints excluded: chain B residue 837 TYR Chi-restraints excluded: chain B residue 849 GLU Chi-restraints excluded: chain B residue 914 HIS Chi-restraints excluded: chain B residue 932 LEU Chi-restraints excluded: chain B residue 979 LEU Chi-restraints excluded: chain B residue 1002 VAL Chi-restraints excluded: chain B residue 1005 LEU Chi-restraints excluded: chain B residue 1056 THR Chi-restraints excluded: chain B residue 1062 THR Chi-restraints excluded: chain B residue 1127 VAL Chi-restraints excluded: chain B residue 1139 ASP Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 129 ASP Chi-restraints excluded: chain A residue 136 HIS Chi-restraints excluded: chain A residue 191 TYR Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 398 ILE Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 595 TRP Chi-restraints excluded: chain A residue 849 GLU Chi-restraints excluded: chain A residue 895 SER Chi-restraints excluded: chain A residue 915 GLU Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain A residue 963 LEU Chi-restraints excluded: chain A residue 979 LEU Chi-restraints excluded: chain A residue 1000 LEU Chi-restraints excluded: chain A residue 1002 VAL Chi-restraints excluded: chain A residue 1005 LEU Chi-restraints excluded: chain A residue 1062 THR Chi-restraints excluded: chain A residue 1127 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 114 optimal weight: 4.9990 chunk 7 optimal weight: 0.7980 chunk 177 optimal weight: 0.6980 chunk 192 optimal weight: 5.9990 chunk 110 optimal weight: 1.9990 chunk 182 optimal weight: 0.6980 chunk 123 optimal weight: 1.9990 chunk 15 optimal weight: 6.9990 chunk 113 optimal weight: 0.9990 chunk 79 optimal weight: 0.9990 chunk 29 optimal weight: 0.5980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B1154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 448 ASN ** A 614 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.115473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.075185 restraints weight = 42604.183| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 3.05 r_work: 0.3029 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3027 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3027 r_free = 0.3027 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3027 r_free = 0.3027 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3027 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.1992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 16244 Z= 0.120 Angle : 0.582 15.183 22054 Z= 0.290 Chirality : 0.039 0.261 2658 Planarity : 0.004 0.078 2754 Dihedral : 7.280 57.919 2368 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.64 % Favored : 95.32 % Rotamer: Outliers : 2.88 % Allowed : 30.47 % Favored : 66.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.11 (0.19), residues: 2094 helix: 2.68 (0.14), residues: 1424 sheet: -0.62 (0.59), residues: 82 loop : -1.70 (0.25), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 609 TYR 0.007 0.001 TYR B 309 PHE 0.025 0.001 PHE B 598 TRP 0.024 0.001 TRP A 643 HIS 0.004 0.001 HIS A1172 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 (16244) covalent geometry : angle 0.58233 / 0.29 (22054) hydrogen bonds : bond 0.04328 / 2.91 ( 1119) hydrogen bonds : angle 3.85555 / 2.89 ( 3309) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 141 time to evaluate : 0.512 Fit side-chains REVERT: B 483 MET cc_start: 0.8972 (mtp) cc_final: 0.8692 (mtp) REVERT: B 512 LEU cc_start: 0.9581 (OUTLIER) cc_final: 0.9100 (mm) REVERT: B 609 ARG cc_start: 0.8875 (ptt180) cc_final: 0.8633 (ptm160) REVERT: B 837 TYR cc_start: 0.8774 (OUTLIER) cc_final: 0.7468 (m-80) REVERT: B 849 GLU cc_start: 0.8904 (OUTLIER) cc_final: 0.8342 (mp0) REVERT: B 924 GLU cc_start: 0.7871 (mp0) cc_final: 0.7200 (mp0) REVERT: B 935 GLU cc_start: 0.8789 (tp30) cc_final: 0.8532 (tp30) REVERT: B 967 MET cc_start: 0.8769 (tpp) cc_final: 0.8322 (tmm) REVERT: B 1139 ASP cc_start: 0.6739 (OUTLIER) cc_final: 0.6123 (p0) REVERT: A 129 ASP cc_start: 0.8213 (OUTLIER) cc_final: 0.7962 (t0) REVERT: A 220 LEU cc_start: 0.8269 (OUTLIER) cc_final: 0.7749 (mp) REVERT: A 512 LEU cc_start: 0.9578 (OUTLIER) cc_final: 0.9092 (mm) REVERT: A 595 TRP cc_start: 0.8509 (OUTLIER) cc_final: 0.7796 (m100) REVERT: A 602 MET cc_start: 0.5994 (mmp) cc_final: 0.5601 (mmp) REVERT: A 849 GLU cc_start: 0.8715 (OUTLIER) cc_final: 0.8254 (mp0) REVERT: A 967 MET cc_start: 0.8721 (tpp) cc_final: 0.8304 (tmm) REVERT: A 1009 TYR cc_start: 0.8231 (t80) cc_final: 0.7894 (t80) outliers start: 45 outliers final: 26 residues processed: 183 average time/residue: 0.0999 time to fit residues: 28.5370 Evaluate side-chains 170 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 135 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 191 TYR Chi-restraints excluded: chain B residue 398 ILE Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 635 TRP Chi-restraints excluded: chain B residue 837 TYR Chi-restraints excluded: chain B residue 849 GLU Chi-restraints excluded: chain B residue 932 LEU Chi-restraints excluded: chain B residue 979 LEU Chi-restraints excluded: chain B residue 1002 VAL Chi-restraints excluded: chain B residue 1005 LEU Chi-restraints excluded: chain B residue 1056 THR Chi-restraints excluded: chain B residue 1062 THR Chi-restraints excluded: chain B residue 1127 VAL Chi-restraints excluded: chain B residue 1139 ASP Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 129 ASP Chi-restraints excluded: chain A residue 136 HIS Chi-restraints excluded: chain A residue 191 TYR Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 398 ILE Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 448 ASN Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 595 TRP Chi-restraints excluded: chain A residue 849 GLU Chi-restraints excluded: chain A residue 915 GLU Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain A residue 963 LEU Chi-restraints excluded: chain A residue 1000 LEU Chi-restraints excluded: chain A residue 1002 VAL Chi-restraints excluded: chain A residue 1005 LEU Chi-restraints excluded: chain A residue 1062 THR Chi-restraints excluded: chain A residue 1127 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 124 optimal weight: 0.5980 chunk 187 optimal weight: 4.9990 chunk 143 optimal weight: 0.9980 chunk 93 optimal weight: 0.4980 chunk 127 optimal weight: 1.9990 chunk 194 optimal weight: 7.9990 chunk 142 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 144 optimal weight: 0.5980 chunk 20 optimal weight: 0.8980 chunk 63 optimal weight: 50.0000 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 448 ASN ** B1154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 448 ASN ** A 614 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.115652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.074484 restraints weight = 59781.493| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 3.62 r_work: 0.3004 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3001 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3001 r_free = 0.3001 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3001 r_free = 0.3001 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3001 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.2076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 16244 Z= 0.121 Angle : 0.593 15.137 22054 Z= 0.293 Chirality : 0.039 0.317 2658 Planarity : 0.004 0.076 2754 Dihedral : 7.225 57.733 2368 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.40 % Favored : 95.55 % Rotamer: Outliers : 2.56 % Allowed : 30.60 % Favored : 66.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.22 (0.19), residues: 2094 helix: 2.70 (0.14), residues: 1422 sheet: 1.16 (0.65), residues: 58 loop : -1.65 (0.25), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 609 TYR 0.007 0.001 TYR A 641 PHE 0.024 0.001 PHE B 598 TRP 0.015 0.001 TRP B 635 HIS 0.004 0.000 HIS A1172 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 (16244) covalent geometry : angle 0.59274 / 0.29 (22054) hydrogen bonds : bond 0.04264 / 2.86 ( 1119) hydrogen bonds : angle 3.85445 / 2.89 ( 3309) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 141 time to evaluate : 0.422 Fit side-chains REVERT: B 483 MET cc_start: 0.9061 (mtp) cc_final: 0.8769 (mtp) REVERT: B 512 LEU cc_start: 0.9550 (OUTLIER) cc_final: 0.9059 (mm) REVERT: B 609 ARG cc_start: 0.8987 (ptt180) cc_final: 0.8720 (ptm160) REVERT: B 837 TYR cc_start: 0.8808 (OUTLIER) cc_final: 0.7387 (m-80) REVERT: B 849 GLU cc_start: 0.8906 (OUTLIER) cc_final: 0.8347 (mp0) REVERT: B 924 GLU cc_start: 0.7887 (mp0) cc_final: 0.7216 (mp0) REVERT: B 935 GLU cc_start: 0.8833 (tp30) cc_final: 0.8574 (tp30) REVERT: B 967 MET cc_start: 0.8749 (tpp) cc_final: 0.8297 (tmm) REVERT: B 1139 ASP cc_start: 0.6515 (OUTLIER) cc_final: 0.6274 (p0) REVERT: A 129 ASP cc_start: 0.8230 (OUTLIER) cc_final: 0.7956 (t0) REVERT: A 220 LEU cc_start: 0.8299 (OUTLIER) cc_final: 0.7783 (mp) REVERT: A 512 LEU cc_start: 0.9555 (OUTLIER) cc_final: 0.9072 (mm) REVERT: A 595 TRP cc_start: 0.8616 (OUTLIER) cc_final: 0.7862 (m100) REVERT: A 602 MET cc_start: 0.6043 (mmp) cc_final: 0.5698 (mmp) REVERT: A 849 GLU cc_start: 0.8717 (OUTLIER) cc_final: 0.8250 (mp0) REVERT: A 967 MET cc_start: 0.8710 (tpp) cc_final: 0.8302 (tmm) REVERT: A 1009 TYR cc_start: 0.8299 (t80) cc_final: 0.7946 (t80) outliers start: 40 outliers final: 30 residues processed: 177 average time/residue: 0.0976 time to fit residues: 27.0125 Evaluate side-chains 176 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 137 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 191 TYR Chi-restraints excluded: chain B residue 398 ILE Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain B residue 448 ASN Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 635 TRP Chi-restraints excluded: chain B residue 837 TYR Chi-restraints excluded: chain B residue 849 GLU Chi-restraints excluded: chain B residue 932 LEU Chi-restraints excluded: chain B residue 979 LEU Chi-restraints excluded: chain B residue 1002 VAL Chi-restraints excluded: chain B residue 1005 LEU Chi-restraints excluded: chain B residue 1056 THR Chi-restraints excluded: chain B residue 1062 THR Chi-restraints excluded: chain B residue 1127 VAL Chi-restraints excluded: chain B residue 1139 ASP Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 129 ASP Chi-restraints excluded: chain A residue 136 HIS Chi-restraints excluded: chain A residue 191 TYR Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 398 ILE Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 448 ASN Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 595 TRP Chi-restraints excluded: chain A residue 635 TRP Chi-restraints excluded: chain A residue 849 GLU Chi-restraints excluded: chain A residue 915 GLU Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain A residue 963 LEU Chi-restraints excluded: chain A residue 979 LEU Chi-restraints excluded: chain A residue 1000 LEU Chi-restraints excluded: chain A residue 1002 VAL Chi-restraints excluded: chain A residue 1005 LEU Chi-restraints excluded: chain A residue 1062 THR Chi-restraints excluded: chain A residue 1118 LYS Chi-restraints excluded: chain A residue 1127 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 25 optimal weight: 0.0370 chunk 94 optimal weight: 0.9980 chunk 95 optimal weight: 0.9990 chunk 161 optimal weight: 50.0000 chunk 143 optimal weight: 7.9990 chunk 89 optimal weight: 1.9990 chunk 38 optimal weight: 0.0000 chunk 88 optimal weight: 1.9990 chunk 135 optimal weight: 2.9990 chunk 54 optimal weight: 0.9990 chunk 61 optimal weight: 50.0000 overall best weight: 0.6066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 448 ASN ** A 614 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.115718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.075088 restraints weight = 46736.329| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 3.20 r_work: 0.3026 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3024 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3024 r_free = 0.3024 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3024 r_free = 0.3024 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3024 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.2078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.224 16244 Z= 0.222 Angle : 0.850 59.200 22054 Z= 0.481 Chirality : 0.041 0.558 2658 Planarity : 0.005 0.189 2754 Dihedral : 7.371 67.611 2368 Min Nonbonded Distance : 1.760 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.40 % Favored : 95.51 % Rotamer: Outliers : 2.50 % Allowed : 30.92 % Favored : 66.58 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.22 (0.19), residues: 2094 helix: 2.70 (0.14), residues: 1422 sheet: 1.17 (0.65), residues: 58 loop : -1.65 (0.25), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 609 TYR 0.008 0.001 TYR A 641 PHE 0.024 0.001 PHE B 598 TRP 0.015 0.001 TRP B 635 HIS 0.004 0.000 HIS A1172 Details of bonding type rmsd/Z covalent geometry : bond 0.00423 / 0.22 (16244) covalent geometry : angle 0.85029 / 0.48 (22054) hydrogen bonds : bond 0.04311 / 2.87 ( 1119) hydrogen bonds : angle 3.85222 / 2.89 ( 3309) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4508.02 seconds wall clock time: 77 minutes 34.89 seconds (4654.89 seconds total)