Starting phenix.real_space_refine on Sat Jul 4 10:34:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mw0_48676/07_2026/9mw0_48676.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mw0_48676/07_2026/9mw0_48676.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.37 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9mw0_48676/07_2026/9mw0_48676.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mw0_48676/07_2026/9mw0_48676.map" model { file = "/net/cci-nas-00/data/ceres_data/9mw0_48676/07_2026/9mw0_48676.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mw0_48676/07_2026/9mw0_48676.cif" } resolution = 3.37 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= 0.019 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 3 5.49 5 S 102 5.16 5 C 12621 2.51 5 N 3264 2.21 5 O 3678 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model 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: 19668 Number of models: 1 Model: "" Number of chains: 9 Chain: "D" Number of atoms: 5943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 784, 5943 Classifications: {'peptide': 784} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 748} Chain breaks: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "G" Number of atoms: 591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 591 Classifications: {'peptide': 79} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 3, 'TRANS': 75} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "E" Number of atoms: 5943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 784, 5943 Classifications: {'peptide': 784} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 748} Chain breaks: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "F" Number of atoms: 5943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 784, 5943 Classifications: {'peptide': 784} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 748} Chain breaks: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "H" Number of atoms: 591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 591 Classifications: {'peptide': 79} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 3, 'TRANS': 75} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "I" Number of atoms: 591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 591 Classifications: {'peptide': 79} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 3, 'TRANS': 75} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "G" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Unusual residues: {'PNS': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Unusual residues: {'PNS': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Unusual residues: {'PNS': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.62, per 1000 atoms: 0.23 Number of scatterers: 19668 At special positions: 0 Unit cell: (126.26, 119.84, 170.13, 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 102 16.00 P 3 15.00 O 3678 8.00 N 3264 7.00 C 12621 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: 1.91 Conformation dependent library (CDL) restraints added in 927.7 milliseconds 5142 Ramachandran restraints generated. 2571 Oldfield, 0 Emsley, 2571 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4800 Finding SS restraints... Secondary structure from input PDB file: 115 helices and 6 sheets defined 74.0% alpha, 5.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'D' and resid 24 through 33 Processing helix chain 'D' and resid 33 through 52 removed outlier: 4.206A pdb=" N VAL D 52 " --> pdb=" O LEU D 48 " (cutoff:3.500A) Processing helix chain 'D' and resid 54 through 62 Processing helix chain 'D' and resid 71 through 84 Processing helix chain 'D' and resid 104 through 121 Processing helix chain 'D' and resid 137 through 142 removed outlier: 3.735A pdb=" N ALA D 141 " --> pdb=" O THR D 137 " (cutoff:3.500A) Processing helix chain 'D' and resid 161 through 178 removed outlier: 4.038A pdb=" N ARG D 178 " --> pdb=" O ILE D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 190 through 226 removed outlier: 4.650A pdb=" N LYS D 207 " --> pdb=" O ASP D 203 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N LEU D 208 " --> pdb=" O ALA D 204 " (cutoff:3.500A) Processing helix chain 'D' and resid 228 through 255 removed outlier: 3.590A pdb=" N TYR D 255 " --> pdb=" O PHE D 251 " (cutoff:3.500A) Processing helix chain 'D' and resid 261 through 294 removed outlier: 3.519A pdb=" N GLY D 294 " --> pdb=" O ALA D 290 " (cutoff:3.500A) Processing helix chain 'D' and resid 296 through 325 removed outlier: 5.165A pdb=" N HIS D 310 " --> pdb=" O HIS D 306 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N VAL D 311 " --> pdb=" O GLY D 307 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 329 Processing helix chain 'D' and resid 331 through 366 removed outlier: 3.578A pdb=" N GLY D 338 " --> pdb=" O PHE D 334 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N VAL D 339 " --> pdb=" O GLN D 335 " (cutoff:3.500A) Proline residue: D 340 - end of helix Proline residue: D 357 - end of helix removed outlier: 3.670A pdb=" N ARG D 365 " --> pdb=" O SER D 361 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N PHE D 366 " --> pdb=" O VAL D 362 " (cutoff:3.500A) Processing helix chain 'D' and resid 378 through 391 Processing helix chain 'D' and resid 391 through 405 removed outlier: 3.657A pdb=" N ILE D 395 " --> pdb=" O TRP D 391 " (cutoff:3.500A) Processing helix chain 'D' and resid 406 through 410 removed outlier: 3.869A pdb=" N ALA D 409 " --> pdb=" O GLY D 406 " (cutoff:3.500A) Processing helix chain 'D' and resid 418 through 423 removed outlier: 3.848A pdb=" N LEU D 423 " --> pdb=" O ARG D 420 " (cutoff:3.500A) Processing helix chain 'D' and resid 427 through 440 Processing helix chain 'D' and resid 441 through 446 removed outlier: 4.048A pdb=" N MET D 445 " --> pdb=" O SER D 441 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ASN D 446 " --> pdb=" O GLN D 442 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 441 through 446' Processing helix chain 'D' and resid 460 through 476 removed outlier: 3.722A pdb=" N VAL D 466 " --> pdb=" O ALA D 462 " (cutoff:3.500A) Processing helix chain 'D' and resid 498 through 503 Processing helix chain 'D' and resid 657 through 685 Processing helix chain 'D' and resid 694 through 699 Processing helix chain 'D' and resid 700 through 711 removed outlier: 3.508A pdb=" N LEU D 709 " --> pdb=" O ARG D 705 " (cutoff:3.500A) Processing helix chain 'D' and resid 730 through 749 removed outlier: 4.565A pdb=" N MET D 737 " --> pdb=" O GLY D 733 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N ASP D 738 " --> pdb=" O THR D 734 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N GLU D 739 " --> pdb=" O ALA D 735 " (cutoff:3.500A) Processing helix chain 'D' and resid 763 through 798 Processing helix chain 'D' and resid 799 through 827 removed outlier: 3.673A pdb=" N ALA D 803 " --> pdb=" O ALA D 799 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N SER D 816 " --> pdb=" O LEU D 812 " (cutoff:3.500A) Processing helix chain 'D' and resid 836 through 864 removed outlier: 4.219A pdb=" N MET D 840 " --> pdb=" O MET D 836 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N VAL D 844 " --> pdb=" O MET D 840 " (cutoff:3.500A) Processing helix chain 'D' and resid 867 through 896 removed outlier: 5.218A pdb=" N ALA D 881 " --> pdb=" O VAL D 877 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N VAL D 882 " --> pdb=" O GLY D 878 " (cutoff:3.500A) Processing helix chain 'D' and resid 897 through 900 Processing helix chain 'D' and resid 902 through 923 removed outlier: 3.845A pdb=" N GLY D 906 " --> pdb=" O LEU D 902 " (cutoff:3.500A) Processing helix chain 'D' and resid 926 through 936 Processing helix chain 'D' and resid 937 through 941 Processing helix chain 'G' and resid 4 through 20 Processing helix chain 'G' and resid 23 through 27 Processing helix chain 'G' and resid 40 through 56 Processing helix chain 'G' and resid 60 through 67 Processing helix chain 'G' and resid 69 through 81 Processing helix chain 'E' and resid 24 through 33 Processing helix chain 'E' and resid 33 through 52 removed outlier: 4.300A pdb=" N VAL E 52 " --> pdb=" O LEU E 48 " (cutoff:3.500A) Processing helix chain 'E' and resid 54 through 62 Processing helix chain 'E' and resid 71 through 84 Processing helix chain 'E' and resid 104 through 121 Processing helix chain 'E' and resid 137 through 142 removed outlier: 3.773A pdb=" N ALA E 141 " --> pdb=" O THR E 137 " (cutoff:3.500A) Processing helix chain 'E' and resid 161 through 178 removed outlier: 4.018A pdb=" N ARG E 178 " --> pdb=" O ILE E 174 " (cutoff:3.500A) Processing helix chain 'E' and resid 190 through 226 removed outlier: 4.684A pdb=" N LYS E 207 " --> pdb=" O ASP E 203 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N LEU E 208 " --> pdb=" O ALA E 204 " (cutoff:3.500A) Processing helix chain 'E' and resid 228 through 255 removed outlier: 3.601A pdb=" N TYR E 255 " --> pdb=" O PHE E 251 " (cutoff:3.500A) Processing helix chain 'E' and resid 261 through 294 Processing helix chain 'E' and resid 296 through 325 removed outlier: 5.170A pdb=" N HIS E 310 " --> pdb=" O HIS E 306 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N VAL E 311 " --> pdb=" O GLY E 307 " (cutoff:3.500A) Processing helix chain 'E' and resid 326 through 329 Processing helix chain 'E' and resid 331 through 366 removed outlier: 3.587A pdb=" N GLY E 338 " --> pdb=" O PHE E 334 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N VAL E 339 " --> pdb=" O GLN E 335 " (cutoff:3.500A) Proline residue: E 340 - end of helix Proline residue: E 357 - end of helix removed outlier: 3.723A pdb=" N ARG E 365 " --> pdb=" O SER E 361 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N PHE E 366 " --> pdb=" O VAL E 362 " (cutoff:3.500A) Processing helix chain 'E' and resid 378 through 391 Processing helix chain 'E' and resid 391 through 405 removed outlier: 3.641A pdb=" N ILE E 395 " --> pdb=" O TRP E 391 " (cutoff:3.500A) Processing helix chain 'E' and resid 406 through 410 removed outlier: 3.800A pdb=" N ALA E 409 " --> pdb=" O GLY E 406 " (cutoff:3.500A) Processing helix chain 'E' and resid 418 through 423 removed outlier: 3.830A pdb=" N LEU E 423 " --> pdb=" O ARG E 420 " (cutoff:3.500A) Processing helix chain 'E' and resid 427 through 440 Processing helix chain 'E' and resid 441 through 446 removed outlier: 4.098A pdb=" N MET E 445 " --> pdb=" O SER E 441 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ASN E 446 " --> pdb=" O GLN E 442 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 441 through 446' Processing helix chain 'E' and resid 460 through 476 removed outlier: 3.742A pdb=" N VAL E 466 " --> pdb=" O ALA E 462 " (cutoff:3.500A) Processing helix chain 'E' and resid 498 through 503 removed outlier: 3.504A pdb=" N THR E 502 " --> pdb=" O THR E 498 " (cutoff:3.500A) Processing helix chain 'E' and resid 657 through 685 Processing helix chain 'E' and resid 694 through 699 Processing helix chain 'E' and resid 700 through 708 Processing helix chain 'E' and resid 730 through 749 removed outlier: 4.605A pdb=" N MET E 737 " --> pdb=" O GLY E 733 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N ASP E 738 " --> pdb=" O THR E 734 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N GLU E 739 " --> pdb=" O ALA E 735 " (cutoff:3.500A) Processing helix chain 'E' and resid 763 through 798 Processing helix chain 'E' and resid 799 through 827 removed outlier: 3.829A pdb=" N ALA E 803 " --> pdb=" O ALA E 799 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N SER E 816 " --> pdb=" O LEU E 812 " (cutoff:3.500A) Processing helix chain 'E' and resid 836 through 864 removed outlier: 4.249A pdb=" N MET E 840 " --> pdb=" O MET E 836 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N VAL E 844 " --> pdb=" O MET E 840 " (cutoff:3.500A) Processing helix chain 'E' and resid 867 through 896 removed outlier: 5.177A pdb=" N ALA E 881 " --> pdb=" O VAL E 877 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N VAL E 882 " --> pdb=" O GLY E 878 " (cutoff:3.500A) Processing helix chain 'E' and resid 897 through 900 Processing helix chain 'E' and resid 902 through 923 removed outlier: 3.738A pdb=" N GLY E 906 " --> pdb=" O LEU E 902 " (cutoff:3.500A) Processing helix chain 'E' and resid 926 through 936 Processing helix chain 'E' and resid 937 through 941 Processing helix chain 'F' and resid 24 through 33 Processing helix chain 'F' and resid 33 through 52 removed outlier: 4.327A pdb=" N VAL F 52 " --> pdb=" O LEU F 48 " (cutoff:3.500A) Processing helix chain 'F' and resid 54 through 62 Processing helix chain 'F' and resid 71 through 84 Processing helix chain 'F' and resid 104 through 121 Processing helix chain 'F' and resid 137 through 142 removed outlier: 3.792A pdb=" N ALA F 141 " --> pdb=" O THR F 137 " (cutoff:3.500A) Processing helix chain 'F' and resid 161 through 178 removed outlier: 4.007A pdb=" N ARG F 178 " --> pdb=" O ILE F 174 " (cutoff:3.500A) Processing helix chain 'F' and resid 190 through 226 removed outlier: 4.671A pdb=" N LYS F 207 " --> pdb=" O ASP F 203 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N LEU F 208 " --> pdb=" O ALA F 204 " (cutoff:3.500A) Processing helix chain 'F' and resid 228 through 255 removed outlier: 3.583A pdb=" N TYR F 255 " --> pdb=" O PHE F 251 " (cutoff:3.500A) Processing helix chain 'F' and resid 261 through 294 Processing helix chain 'F' and resid 296 through 325 removed outlier: 5.169A pdb=" N HIS F 310 " --> pdb=" O HIS F 306 " (cutoff:3.500A) removed outlier: 5.227A pdb=" N VAL F 311 " --> pdb=" O GLY F 307 " (cutoff:3.500A) Processing helix chain 'F' and resid 326 through 329 Processing helix chain 'F' and resid 331 through 366 removed outlier: 3.589A pdb=" N GLY F 338 " --> pdb=" O PHE F 334 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N VAL F 339 " --> pdb=" O GLN F 335 " (cutoff:3.500A) Proline residue: F 340 - end of helix Proline residue: F 357 - end of helix removed outlier: 3.705A pdb=" N ARG F 365 " --> pdb=" O SER F 361 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N PHE F 366 " --> pdb=" O VAL F 362 " (cutoff:3.500A) Processing helix chain 'F' and resid 378 through 391 Processing helix chain 'F' and resid 391 through 405 removed outlier: 3.645A pdb=" N ILE F 395 " --> pdb=" O TRP F 391 " (cutoff:3.500A) Processing helix chain 'F' and resid 406 through 410 removed outlier: 3.828A pdb=" N ALA F 409 " --> pdb=" O GLY F 406 " (cutoff:3.500A) Processing helix chain 'F' and resid 418 through 423 removed outlier: 3.831A pdb=" N LEU F 423 " --> pdb=" O ARG F 420 " (cutoff:3.500A) Processing helix chain 'F' and resid 427 through 440 removed outlier: 4.040A pdb=" N HIS F 439 " --> pdb=" O ALA F 435 " (cutoff:3.500A) Processing helix chain 'F' and resid 441 through 446 removed outlier: 4.077A pdb=" N MET F 445 " --> pdb=" O SER F 441 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ASN F 446 " --> pdb=" O GLN F 442 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 441 through 446' Processing helix chain 'F' and resid 460 through 476 removed outlier: 3.748A pdb=" N VAL F 466 " --> pdb=" O ALA F 462 " (cutoff:3.500A) Processing helix chain 'F' and resid 498 through 503 removed outlier: 3.516A pdb=" N THR F 502 " --> pdb=" O THR F 498 " (cutoff:3.500A) Processing helix chain 'F' and resid 657 through 685 Processing helix chain 'F' and resid 694 through 700 removed outlier: 3.777A pdb=" N PHE F 698 " --> pdb=" O PRO F 694 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLU F 699 " --> pdb=" O PRO F 695 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N THR F 700 " --> pdb=" O GLU F 696 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 694 through 700' Processing helix chain 'F' and resid 700 through 708 Processing helix chain 'F' and resid 730 through 749 removed outlier: 4.591A pdb=" N MET F 737 " --> pdb=" O GLY F 733 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N ASP F 738 " --> pdb=" O THR F 734 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N GLU F 739 " --> pdb=" O ALA F 735 " (cutoff:3.500A) Processing helix chain 'F' and resid 763 through 798 Processing helix chain 'F' and resid 799 through 827 removed outlier: 3.692A pdb=" N ALA F 803 " --> pdb=" O ALA F 799 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N SER F 816 " --> pdb=" O LEU F 812 " (cutoff:3.500A) Processing helix chain 'F' and resid 836 through 863 removed outlier: 4.211A pdb=" N MET F 840 " --> pdb=" O MET F 836 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N VAL F 844 " --> pdb=" O MET F 840 " (cutoff:3.500A) Processing helix chain 'F' and resid 864 through 866 No H-bonds generated for 'chain 'F' and resid 864 through 866' Processing helix chain 'F' and resid 867 through 896 removed outlier: 5.203A pdb=" N ALA F 881 " --> pdb=" O VAL F 877 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N VAL F 882 " --> pdb=" O GLY F 878 " (cutoff:3.500A) Processing helix chain 'F' and resid 897 through 900 Processing helix chain 'F' and resid 902 through 923 removed outlier: 3.798A pdb=" N GLY F 906 " --> pdb=" O LEU F 902 " (cutoff:3.500A) Processing helix chain 'F' and resid 926 through 936 Processing helix chain 'F' and resid 937 through 941 Processing helix chain 'H' and resid 4 through 20 Processing helix chain 'H' and resid 23 through 27 Processing helix chain 'H' and resid 40 through 56 Processing helix chain 'H' and resid 60 through 67 Processing helix chain 'H' and resid 69 through 81 Processing helix chain 'I' and resid 4 through 20 Processing helix chain 'I' and resid 23 through 27 Processing helix chain 'I' and resid 40 through 56 Processing helix chain 'I' and resid 60 through 67 Processing helix chain 'I' and resid 69 through 81 Processing sheet with id=AA1, first strand: chain 'D' and resid 125 through 129 removed outlier: 3.863A pdb=" N HIS D 127 " --> pdb=" O TYR D 154 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N GLN D 152 " --> pdb=" O GLN D 129 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N SER D 91 " --> pdb=" O ILE D 155 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 480 through 484 removed outlier: 3.509A pdb=" N GLN D 482 " --> pdb=" O ILE D 723 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 125 through 129 removed outlier: 3.852A pdb=" N HIS E 127 " --> pdb=" O TYR E 154 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N GLN E 152 " --> pdb=" O GLN E 129 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N SER E 91 " --> pdb=" O ILE E 155 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 480 through 484 removed outlier: 3.507A pdb=" N GLN E 482 " --> pdb=" O ILE E 723 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'F' and resid 125 through 129 removed outlier: 3.861A pdb=" N HIS F 127 " --> pdb=" O TYR F 154 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N GLN F 152 " --> pdb=" O GLN F 129 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N SER F 91 " --> pdb=" O ILE F 155 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 480 through 484 removed outlier: 3.505A pdb=" N GLN F 482 " --> pdb=" O ILE F 723 " (cutoff:3.500A) 1458 hydrogen bonds defined for protein. 4257 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.66 Time building geometry restraints manager: 2.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 6426 1.35 - 1.47: 4575 1.47 - 1.59: 8859 1.59 - 1.72: 3 1.72 - 1.84: 198 Bond restraints: 20061 Sorted by residual: bond pdb=" O27 PNS G 101 " pdb=" P24 PNS G 101 " ideal model delta sigma weight residual 1.704 1.842 -0.138 2.00e-02 2.50e+03 4.75e+01 bond pdb=" O27 PNS F1001 " pdb=" P24 PNS F1001 " ideal model delta sigma weight residual 1.704 1.842 -0.138 2.00e-02 2.50e+03 4.75e+01 bond pdb=" O27 PNS E1001 " pdb=" P24 PNS E1001 " ideal model delta sigma weight residual 1.704 1.841 -0.137 2.00e-02 2.50e+03 4.70e+01 bond pdb=" C34 PNS G 101 " pdb=" N36 PNS G 101 " ideal model delta sigma weight residual 1.337 1.412 -0.075 2.00e-02 2.50e+03 1.40e+01 bond pdb=" C34 PNS F1001 " pdb=" N36 PNS F1001 " ideal model delta sigma weight residual 1.337 1.411 -0.074 2.00e-02 2.50e+03 1.37e+01 ... (remaining 20056 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.56: 26961 1.56 - 3.13: 319 3.13 - 4.69: 57 4.69 - 6.26: 26 6.26 - 7.82: 6 Bond angle restraints: 27369 Sorted by residual: angle pdb=" C GLY F 338 " pdb=" N VAL F 339 " pdb=" CA VAL F 339 " ideal model delta sigma weight residual 120.33 122.61 -2.28 8.00e-01 1.56e+00 8.09e+00 angle pdb=" C VAL F 339 " pdb=" CA VAL F 339 " pdb=" CB VAL F 339 " ideal model delta sigma weight residual 114.00 110.37 3.63 1.31e+00 5.83e-01 7.68e+00 angle pdb=" C VAL D 339 " pdb=" CA VAL D 339 " pdb=" CB VAL D 339 " ideal model delta sigma weight residual 114.00 110.37 3.63 1.31e+00 5.83e-01 7.68e+00 angle pdb=" C VAL E 339 " pdb=" CA VAL E 339 " pdb=" CB VAL E 339 " ideal model delta sigma weight residual 114.00 110.38 3.62 1.31e+00 5.83e-01 7.64e+00 angle pdb=" C ALA D 34 " pdb=" N VAL D 35 " pdb=" CA VAL D 35 " ideal model delta sigma weight residual 120.33 122.54 -2.21 8.00e-01 1.56e+00 7.62e+00 ... (remaining 27364 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.41: 11031 13.41 - 26.81: 664 26.81 - 40.22: 143 40.22 - 53.62: 50 53.62 - 67.03: 7 Dihedral angle restraints: 11895 sinusoidal: 4437 harmonic: 7458 Sorted by residual: dihedral pdb=" CA ASP E 134 " pdb=" CB ASP E 134 " pdb=" CG ASP E 134 " pdb=" OD1 ASP E 134 " ideal model delta sinusoidal sigma weight residual -30.00 -86.40 56.40 1 2.00e+01 2.50e-03 1.07e+01 dihedral pdb=" CA VAL E 837 " pdb=" C VAL E 837 " pdb=" N LEU E 838 " pdb=" CA LEU E 838 " ideal model delta harmonic sigma weight residual -180.00 -163.69 -16.31 0 5.00e+00 4.00e-02 1.06e+01 dihedral pdb=" CA ASP D 134 " pdb=" CB ASP D 134 " pdb=" CG ASP D 134 " pdb=" OD1 ASP D 134 " ideal model delta sinusoidal sigma weight residual -30.00 -85.90 55.90 1 2.00e+01 2.50e-03 1.05e+01 ... (remaining 11892 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 2412 0.038 - 0.076: 667 0.076 - 0.114: 182 0.114 - 0.152: 12 0.152 - 0.190: 3 Chirality restraints: 3276 Sorted by residual: chirality pdb=" C32 PNS F1001 " pdb=" C29 PNS F1001 " pdb=" C34 PNS F1001 " pdb=" O33 PNS F1001 " both_signs ideal model delta sigma weight residual False 2.33 2.52 -0.19 2.00e-01 2.50e+01 9.00e-01 chirality pdb=" C32 PNS E1001 " pdb=" C29 PNS E1001 " pdb=" C34 PNS E1001 " pdb=" O33 PNS E1001 " both_signs ideal model delta sigma weight residual False 2.33 2.51 -0.19 2.00e-01 2.50e+01 8.79e-01 chirality pdb=" C32 PNS G 101 " pdb=" C29 PNS G 101 " pdb=" C34 PNS G 101 " pdb=" O33 PNS G 101 " both_signs ideal model delta sigma weight residual False 2.33 2.51 -0.19 2.00e-01 2.50e+01 8.70e-01 ... (remaining 3273 not shown) Planarity restraints: 3477 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR D 751 " -0.022 5.00e-02 4.00e+02 3.28e-02 1.72e+00 pdb=" N PRO D 752 " 0.057 5.00e-02 4.00e+02 pdb=" CA PRO D 752 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO D 752 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR F 751 " 0.021 5.00e-02 4.00e+02 3.22e-02 1.66e+00 pdb=" N PRO F 752 " -0.056 5.00e-02 4.00e+02 pdb=" CA PRO F 752 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO F 752 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR E 751 " -0.021 5.00e-02 4.00e+02 3.21e-02 1.65e+00 pdb=" N PRO E 752 " 0.056 5.00e-02 4.00e+02 pdb=" CA PRO E 752 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO E 752 " -0.018 5.00e-02 4.00e+02 ... (remaining 3474 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 4604 2.79 - 3.32: 20284 3.32 - 3.84: 33221 3.84 - 4.37: 37188 4.37 - 4.90: 65849 Nonbonded interactions: 161146 Sorted by model distance: nonbonded pdb=" O GLU F 673 " pdb=" OG1 THR F 676 " model vdw 2.260 3.040 nonbonded pdb=" O MET D 304 " pdb=" OG1 THR D 308 " model vdw 2.260 3.040 nonbonded pdb=" O ALA E 866 " pdb=" OG1 THR E 870 " model vdw 2.278 3.040 nonbonded pdb=" OH TYR D 422 " pdb=" O PRO D 832 " model vdw 2.283 3.040 nonbonded pdb=" O ALA F 866 " pdb=" OG1 THR F 870 " model vdw 2.286 3.040 ... (remaining 161141 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'D' selection = (chain 'E' and resid 22 through 957) selection = (chain 'F' and resid 22 through 957) } ncs_group { reference = (chain 'G' and resid 3 through 81) selection = chain 'H' selection = chain 'I' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 19.300 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.138 20061 Z= 0.183 Angle : 0.509 7.822 27369 Z= 0.285 Chirality : 0.038 0.190 3276 Planarity : 0.003 0.033 3477 Dihedral : 9.727 67.029 7095 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 1.80 % Allowed : 4.92 % Favored : 93.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: 3.68 (0.17), residues: 2571 helix: 3.03 (0.12), residues: 1710 sheet: 1.15 (0.44), residues: 153 loop : 1.33 (0.25), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 924 TYR 0.012 0.001 TYR F 776 PHE 0.009 0.001 PHE D 703 TRP 0.007 0.001 TRP E 381 HIS 0.003 0.001 HIS D 827 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.18 (20061) covalent geometry : angle 0.50869 / 0.29 (27369) hydrogen bonds : bond 0.14584 / 10.08 ( 1458) hydrogen bonds : angle 5.50742 / 3.97 ( 4257) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5142 Ramachandran restraints generated. 2571 Oldfield, 0 Emsley, 2571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5142 Ramachandran restraints generated. 2571 Oldfield, 0 Emsley, 2571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 606 residues out of total 2073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 569 time to evaluate : 0.679 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 25 ARG cc_start: 0.6898 (OUTLIER) cc_final: 0.4821 (mpp-170) REVERT: D 738 ASP cc_start: 0.7268 (OUTLIER) cc_final: 0.7026 (m-30) REVERT: G 52 GLU cc_start: 0.8348 (tt0) cc_final: 0.7468 (tt0) REVERT: E 25 ARG cc_start: 0.7311 (OUTLIER) cc_final: 0.6310 (mpp-170) REVERT: F 25 ARG cc_start: 0.7149 (OUTLIER) cc_final: 0.4762 (mpp-170) REVERT: F 445 MET cc_start: 0.8385 (mmp) cc_final: 0.8164 (mmp) REVERT: H 15 ILE cc_start: 0.9274 (mt) cc_final: 0.9018 (mm) REVERT: H 23 GLU cc_start: 0.8192 (pm20) cc_final: 0.7524 (pm20) REVERT: H 52 GLU cc_start: 0.8368 (tt0) cc_final: 0.7825 (tt0) REVERT: H 78 GLN cc_start: 0.8743 (mt0) cc_final: 0.8452 (mt0) REVERT: I 15 ILE cc_start: 0.9291 (mt) cc_final: 0.9001 (mm) REVERT: I 23 GLU cc_start: 0.8163 (pm20) cc_final: 0.7265 (pm20) outliers start: 37 outliers final: 10 residues processed: 594 average time/residue: 0.1349 time to fit residues: 125.3555 Evaluate side-chains 414 residues out of total 2073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 400 time to evaluate : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 25 ARG Chi-restraints excluded: chain D residue 123 GLU Chi-restraints excluded: chain D residue 130 ASP Chi-restraints excluded: chain D residue 419 ASP Chi-restraints excluded: chain D residue 738 ASP Chi-restraints excluded: chain E residue 25 ARG Chi-restraints excluded: chain E residue 130 ASP Chi-restraints excluded: chain E residue 262 THR Chi-restraints excluded: chain E residue 738 ASP Chi-restraints excluded: chain F residue 25 ARG Chi-restraints excluded: chain F residue 130 ASP Chi-restraints excluded: chain F residue 151 VAL Chi-restraints excluded: chain F residue 738 ASP Chi-restraints excluded: chain H residue 35 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 216 optimal weight: 0.8980 chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 4.9990 chunk 227 optimal weight: 10.0000 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.7980 chunk 247 optimal weight: 0.9980 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 0.4980 chunk 103 optimal weight: 0.0270 overall best weight: 0.5838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 82 GLN D 430 ASN D 439 HIS D 482 GLN D 672 GLN E 82 GLN E 430 ASN E 482 GLN F 82 GLN F 129 GLN F 430 ASN F 482 GLN F 672 GLN H 78 GLN I 78 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.081482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.069847 restraints weight = 52709.179| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 3.12 r_work: 0.2980 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.2074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 20061 Z= 0.132 Angle : 0.543 6.997 27369 Z= 0.284 Chirality : 0.041 0.166 3276 Planarity : 0.004 0.056 3477 Dihedral : 4.423 62.421 2829 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 2.34 % Allowed : 13.94 % Favored : 83.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: 3.39 (0.16), residues: 2571 helix: 2.71 (0.12), residues: 1764 sheet: 1.41 (0.42), residues: 156 loop : 1.27 (0.26), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 178 TYR 0.015 0.001 TYR E 111 PHE 0.016 0.001 PHE E 375 TRP 0.008 0.001 TRP E 825 HIS 0.003 0.001 HIS E 124 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.13 (20061) covalent geometry : angle 0.54274 / 0.28 (27369) hydrogen bonds : bond 0.05008 / 3.44 ( 1458) hydrogen bonds : angle 4.36798 / 3.18 ( 4257) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5142 Ramachandran restraints generated. 2571 Oldfield, 0 Emsley, 2571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5142 Ramachandran restraints generated. 2571 Oldfield, 0 Emsley, 2571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 473 residues out of total 2073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 425 time to evaluate : 0.689 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 25 ARG cc_start: 0.8370 (OUTLIER) cc_final: 0.7305 (mpp-170) REVERT: D 676 THR cc_start: 0.9571 (p) cc_final: 0.9078 (t) REVERT: G 7 GLU cc_start: 0.9072 (mt-10) cc_final: 0.8774 (pt0) REVERT: G 17 GLU cc_start: 0.8887 (tp30) cc_final: 0.8647 (tp30) REVERT: G 18 GLU cc_start: 0.8821 (tm-30) cc_final: 0.8616 (tm-30) REVERT: G 23 GLU cc_start: 0.8737 (pm20) cc_final: 0.7902 (pm20) REVERT: G 26 GLU cc_start: 0.8906 (tt0) cc_final: 0.8610 (mt-10) REVERT: G 54 LYS cc_start: 0.9076 (tptp) cc_final: 0.8831 (tptp) REVERT: E 173 LYS cc_start: 0.9547 (tppt) cc_final: 0.9302 (ttpp) REVERT: E 177 GLU cc_start: 0.8491 (pp20) cc_final: 0.8268 (pp20) REVERT: E 676 THR cc_start: 0.9361 (p) cc_final: 0.9031 (t) REVERT: F 94 MET cc_start: 0.8324 (mtt) cc_final: 0.8119 (mtp) REVERT: F 101 GLU cc_start: 0.8969 (mm-30) cc_final: 0.8396 (pm20) REVERT: F 177 GLU cc_start: 0.8304 (pp20) cc_final: 0.8092 (pp20) REVERT: H 23 GLU cc_start: 0.8837 (pm20) cc_final: 0.8196 (pm20) REVERT: H 26 GLU cc_start: 0.9154 (tt0) cc_final: 0.8901 (mt-10) REVERT: H 31 LYS cc_start: 0.8372 (mmmm) cc_final: 0.8001 (mmmm) REVERT: H 54 LYS cc_start: 0.9004 (tptp) cc_final: 0.8732 (tptp) REVERT: H 67 LEU cc_start: 0.8199 (mm) cc_final: 0.7832 (mm) REVERT: I 17 GLU cc_start: 0.8721 (tp30) cc_final: 0.8158 (tp30) REVERT: I 54 LYS cc_start: 0.8973 (tptp) cc_final: 0.8772 (tptp) outliers start: 48 outliers final: 29 residues processed: 455 average time/residue: 0.1262 time to fit residues: 91.3425 Evaluate side-chains 411 residues out of total 2073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 381 time to evaluate : 0.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 25 ARG Chi-restraints excluded: chain D residue 123 GLU Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 404 LEU Chi-restraints excluded: chain D residue 748 ILE Chi-restraints excluded: chain G residue 62 GLU Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 198 GLN Chi-restraints excluded: chain E residue 239 VAL Chi-restraints excluded: chain E residue 252 LEU Chi-restraints excluded: chain E residue 331 LEU Chi-restraints excluded: chain E residue 404 LEU Chi-restraints excluded: chain E residue 748 ILE Chi-restraints excluded: chain E residue 930 SER Chi-restraints excluded: chain F residue 25 ARG Chi-restraints excluded: chain F residue 182 SER Chi-restraints excluded: chain F residue 239 VAL Chi-restraints excluded: chain F residue 252 LEU Chi-restraints excluded: chain F residue 353 LEU Chi-restraints excluded: chain F residue 404 LEU Chi-restraints excluded: chain F residue 748 ILE Chi-restraints excluded: chain F residue 787 ILE Chi-restraints excluded: chain F residue 930 SER Chi-restraints excluded: chain H residue 27 VAL Chi-restraints excluded: chain H residue 62 GLU Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain I residue 27 VAL Chi-restraints excluded: chain I residue 62 GLU Chi-restraints excluded: chain I residue 70 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 79 optimal weight: 5.9990 chunk 63 optimal weight: 3.9990 chunk 16 optimal weight: 10.0000 chunk 121 optimal weight: 4.9990 chunk 126 optimal weight: 0.7980 chunk 2 optimal weight: 4.9990 chunk 184 optimal weight: 3.9990 chunk 75 optimal weight: 0.7980 chunk 254 optimal weight: 0.7980 chunk 41 optimal weight: 0.6980 chunk 4 optimal weight: 4.9990 overall best weight: 1.4182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 661 GLN E 672 GLN F 430 ASN I 78 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.079705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.068134 restraints weight = 53809.877| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 3.15 r_work: 0.2944 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.2317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 20061 Z= 0.164 Angle : 0.545 8.226 27369 Z= 0.284 Chirality : 0.041 0.222 3276 Planarity : 0.004 0.065 3477 Dihedral : 4.331 61.484 2807 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 3.12 % Allowed : 14.57 % Favored : 82.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: 3.19 (0.17), residues: 2571 helix: 2.56 (0.12), residues: 1761 sheet: 1.17 (0.43), residues: 171 loop : 1.24 (0.26), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 421 TYR 0.014 0.001 TYR E 111 PHE 0.014 0.001 PHE E 892 TRP 0.006 0.001 TRP E 381 HIS 0.003 0.001 HIS E 124 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.16 (20061) covalent geometry : angle 0.54506 / 0.28 (27369) hydrogen bonds : bond 0.04986 / 3.43 ( 1458) hydrogen bonds : angle 4.26330 / 3.10 ( 4257) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5142 Ramachandran restraints generated. 2571 Oldfield, 0 Emsley, 2571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5142 Ramachandran restraints generated. 2571 Oldfield, 0 Emsley, 2571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 2073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 394 time to evaluate : 0.767 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 100 GLU cc_start: 0.8293 (mp0) cc_final: 0.8056 (pm20) REVERT: D 267 MET cc_start: 0.9069 (mmp) cc_final: 0.8773 (mmm) REVERT: G 7 GLU cc_start: 0.9094 (mt-10) cc_final: 0.8626 (pt0) REVERT: G 17 GLU cc_start: 0.8809 (tp30) cc_final: 0.8567 (tp30) REVERT: G 23 GLU cc_start: 0.8770 (pm20) cc_final: 0.8040 (pm20) REVERT: G 26 GLU cc_start: 0.8893 (tt0) cc_final: 0.8507 (mt-10) REVERT: G 54 LYS cc_start: 0.8983 (tptp) cc_final: 0.8769 (tptp) REVERT: E 337 MET cc_start: 0.9410 (tpp) cc_final: 0.9161 (tpp) REVERT: F 100 GLU cc_start: 0.8421 (mp0) cc_final: 0.8174 (pm20) REVERT: F 101 GLU cc_start: 0.8983 (mm-30) cc_final: 0.8395 (pm20) REVERT: H 23 GLU cc_start: 0.8851 (pm20) cc_final: 0.8295 (pm20) REVERT: H 26 GLU cc_start: 0.9109 (tt0) cc_final: 0.8722 (mt-10) REVERT: H 31 LYS cc_start: 0.8291 (mmmm) cc_final: 0.8005 (mmmm) REVERT: H 54 LYS cc_start: 0.8991 (tptp) cc_final: 0.8720 (tptp) REVERT: H 67 LEU cc_start: 0.8130 (mm) cc_final: 0.7594 (mm) REVERT: I 17 GLU cc_start: 0.8703 (tp30) cc_final: 0.8084 (tp30) outliers start: 64 outliers final: 43 residues processed: 429 average time/residue: 0.1272 time to fit residues: 87.3313 Evaluate side-chains 408 residues out of total 2073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 365 time to evaluate : 0.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 25 ARG Chi-restraints excluded: chain D residue 182 SER Chi-restraints excluded: chain D residue 231 THR Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 271 LEU Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain D residue 404 LEU Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 680 GLN Chi-restraints excluded: chain D residue 748 ILE Chi-restraints excluded: chain D residue 921 LEU Chi-restraints excluded: chain D residue 925 SER Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 62 GLU Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain E residue 25 ARG Chi-restraints excluded: chain E residue 198 GLN Chi-restraints excluded: chain E residue 239 VAL Chi-restraints excluded: chain E residue 252 LEU Chi-restraints excluded: chain E residue 331 LEU Chi-restraints excluded: chain E residue 353 LEU Chi-restraints excluded: chain E residue 401 VAL Chi-restraints excluded: chain E residue 483 VAL Chi-restraints excluded: chain E residue 925 SER Chi-restraints excluded: chain E residue 930 SER Chi-restraints excluded: chain F residue 25 ARG Chi-restraints excluded: chain F residue 231 THR Chi-restraints excluded: chain F residue 239 VAL Chi-restraints excluded: chain F residue 252 LEU Chi-restraints excluded: chain F residue 268 VAL Chi-restraints excluded: chain F residue 353 LEU Chi-restraints excluded: chain F residue 401 VAL Chi-restraints excluded: chain F residue 466 VAL Chi-restraints excluded: chain F residue 483 VAL Chi-restraints excluded: chain F residue 787 ILE Chi-restraints excluded: chain F residue 925 SER Chi-restraints excluded: chain F residue 930 SER Chi-restraints excluded: chain H residue 27 VAL Chi-restraints excluded: chain H residue 62 GLU Chi-restraints excluded: chain I residue 27 VAL Chi-restraints excluded: chain I residue 62 GLU Chi-restraints excluded: chain I residue 70 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 225 optimal weight: 2.9990 chunk 196 optimal weight: 2.9990 chunk 87 optimal weight: 4.9990 chunk 190 optimal weight: 6.9990 chunk 208 optimal weight: 3.9990 chunk 131 optimal weight: 4.9990 chunk 133 optimal weight: 10.0000 chunk 121 optimal weight: 3.9990 chunk 79 optimal weight: 3.9990 chunk 35 optimal weight: 0.3980 chunk 197 optimal weight: 3.9990 overall best weight: 2.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 382 HIS E 382 HIS E 661 GLN F 382 HIS F 430 ASN F 482 GLN I 78 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.077209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.065678 restraints weight = 54681.765| |-----------------------------------------------------------------------------| r_work (start): 0.3016 rms_B_bonded: 3.11 r_work: 0.2890 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8605 moved from start: 0.2556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 20061 Z= 0.280 Angle : 0.630 9.130 27369 Z= 0.329 Chirality : 0.043 0.163 3276 Planarity : 0.005 0.059 3477 Dihedral : 4.394 42.908 2804 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 4.63 % Allowed : 14.77 % Favored : 80.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: 2.88 (0.17), residues: 2571 helix: 2.32 (0.12), residues: 1752 sheet: 1.51 (0.43), residues: 156 loop : 1.03 (0.25), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 178 TYR 0.015 0.002 TYR F 776 PHE 0.018 0.002 PHE H 33 TRP 0.007 0.001 TRP F 825 HIS 0.006 0.001 HIS D 439 Details of bonding type rmsd/Z covalent geometry : bond 0.00644 / 0.28 (20061) covalent geometry : angle 0.63046 / 0.33 (27369) hydrogen bonds : bond 0.05677 / 3.90 ( 1458) hydrogen bonds : angle 4.47521 / 3.26 ( 4257) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5142 Ramachandran restraints generated. 2571 Oldfield, 0 Emsley, 2571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5142 Ramachandran restraints generated. 2571 Oldfield, 0 Emsley, 2571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 461 residues out of total 2073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 366 time to evaluate : 0.640 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 100 GLU cc_start: 0.8252 (mp0) cc_final: 0.7866 (pm20) REVERT: D 225 TYR cc_start: 0.9178 (m-10) cc_final: 0.8904 (m-10) REVERT: D 267 MET cc_start: 0.9140 (mmp) cc_final: 0.8754 (mmm) REVERT: D 337 MET cc_start: 0.9432 (tpp) cc_final: 0.8901 (tpt) REVERT: D 451 MET cc_start: 0.9261 (ttp) cc_final: 0.8851 (ttp) REVERT: G 23 GLU cc_start: 0.8795 (pm20) cc_final: 0.8062 (pm20) REVERT: G 26 GLU cc_start: 0.8989 (tt0) cc_final: 0.8599 (mt-10) REVERT: G 58 LYS cc_start: 0.8585 (tptt) cc_final: 0.8285 (tptt) REVERT: G 67 LEU cc_start: 0.8241 (mm) cc_final: 0.7985 (mm) REVERT: E 225 TYR cc_start: 0.9120 (m-10) cc_final: 0.8866 (m-10) REVERT: E 337 MET cc_start: 0.9436 (tpp) cc_final: 0.9235 (tpp) REVERT: F 94 MET cc_start: 0.8355 (mtp) cc_final: 0.8154 (mtp) REVERT: F 100 GLU cc_start: 0.8397 (mp0) cc_final: 0.8096 (pm20) REVERT: F 101 GLU cc_start: 0.9073 (mm-30) cc_final: 0.8423 (pm20) REVERT: F 225 TYR cc_start: 0.9143 (m-10) cc_final: 0.8782 (m-10) REVERT: H 23 GLU cc_start: 0.8946 (pm20) cc_final: 0.8741 (pm20) REVERT: H 54 LYS cc_start: 0.9002 (tptp) cc_final: 0.8749 (tptp) REVERT: H 67 LEU cc_start: 0.8136 (mm) cc_final: 0.7713 (mm) REVERT: H 78 GLN cc_start: 0.9479 (mt0) cc_final: 0.9243 (mt0) REVERT: I 17 GLU cc_start: 0.8733 (tp30) cc_final: 0.8060 (tp30) REVERT: I 23 GLU cc_start: 0.8578 (pm20) cc_final: 0.8360 (pm20) REVERT: I 26 GLU cc_start: 0.8998 (tt0) cc_final: 0.8721 (mt-10) REVERT: I 67 LEU cc_start: 0.8655 (mp) cc_final: 0.8253 (mm) outliers start: 95 outliers final: 74 residues processed: 422 average time/residue: 0.1139 time to fit residues: 77.5367 Evaluate side-chains 432 residues out of total 2073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 358 time to evaluate : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 25 ARG Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 231 THR Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 268 VAL Chi-restraints excluded: chain D residue 271 LEU Chi-restraints excluded: chain D residue 281 ILE Chi-restraints excluded: chain D residue 360 ILE Chi-restraints excluded: chain D residue 398 CYS Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain D residue 404 LEU Chi-restraints excluded: chain D residue 455 ASP Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 787 ILE Chi-restraints excluded: chain D residue 788 LEU Chi-restraints excluded: chain D residue 921 LEU Chi-restraints excluded: chain D residue 925 SER Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 62 GLU Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain E residue 25 ARG Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 151 VAL Chi-restraints excluded: chain E residue 198 GLN Chi-restraints excluded: chain E residue 231 THR Chi-restraints excluded: chain E residue 239 VAL Chi-restraints excluded: chain E residue 252 LEU Chi-restraints excluded: chain E residue 262 THR Chi-restraints excluded: chain E residue 268 VAL Chi-restraints excluded: chain E residue 271 LEU Chi-restraints excluded: chain E residue 281 ILE Chi-restraints excluded: chain E residue 284 ILE Chi-restraints excluded: chain E residue 353 LEU Chi-restraints excluded: chain E residue 401 VAL Chi-restraints excluded: chain E residue 455 ASP Chi-restraints excluded: chain E residue 466 VAL Chi-restraints excluded: chain E residue 483 VAL Chi-restraints excluded: chain E residue 787 ILE Chi-restraints excluded: chain E residue 860 MET Chi-restraints excluded: chain E residue 921 LEU Chi-restraints excluded: chain E residue 925 SER Chi-restraints excluded: chain E residue 930 SER Chi-restraints excluded: chain F residue 25 ARG Chi-restraints excluded: chain F residue 45 VAL Chi-restraints excluded: chain F residue 231 THR Chi-restraints excluded: chain F residue 239 VAL Chi-restraints excluded: chain F residue 252 LEU Chi-restraints excluded: chain F residue 268 VAL Chi-restraints excluded: chain F residue 271 LEU Chi-restraints excluded: chain F residue 281 ILE Chi-restraints excluded: chain F residue 353 LEU Chi-restraints excluded: chain F residue 401 VAL Chi-restraints excluded: chain F residue 404 LEU Chi-restraints excluded: chain F residue 455 ASP Chi-restraints excluded: chain F residue 466 VAL Chi-restraints excluded: chain F residue 483 VAL Chi-restraints excluded: chain F residue 495 GLU Chi-restraints excluded: chain F residue 787 ILE Chi-restraints excluded: chain F residue 921 LEU Chi-restraints excluded: chain F residue 925 SER Chi-restraints excluded: chain F residue 930 SER Chi-restraints excluded: chain H residue 16 ILE Chi-restraints excluded: chain H residue 27 VAL Chi-restraints excluded: chain H residue 35 ASP Chi-restraints excluded: chain H residue 59 ILE Chi-restraints excluded: chain H residue 62 GLU Chi-restraints excluded: chain I residue 14 GLU Chi-restraints excluded: chain I residue 22 ILE Chi-restraints excluded: chain I residue 27 VAL Chi-restraints excluded: chain I residue 62 GLU Chi-restraints excluded: chain I residue 64 LEU Chi-restraints excluded: chain I residue 70 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 180 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 155 optimal weight: 0.0980 chunk 38 optimal weight: 3.9990 chunk 90 optimal weight: 0.7980 chunk 214 optimal weight: 0.9980 chunk 1 optimal weight: 0.9980 chunk 186 optimal weight: 0.8980 chunk 191 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 31 optimal weight: 5.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 661 GLN F 430 ASN F 482 GLN I 78 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.080326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.068667 restraints weight = 53301.216| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 3.14 r_work: 0.2959 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.2713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 20061 Z= 0.126 Angle : 0.538 10.668 27369 Z= 0.276 Chirality : 0.041 0.204 3276 Planarity : 0.004 0.053 3477 Dihedral : 4.255 42.128 2804 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 2.63 % Allowed : 16.81 % Favored : 80.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: 3.02 (0.17), residues: 2571 helix: 2.41 (0.12), residues: 1752 sheet: 1.67 (0.43), residues: 156 loop : 1.07 (0.25), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 178 TYR 0.027 0.001 TYR I 76 PHE 0.010 0.001 PHE D 703 TRP 0.007 0.001 TRP F 381 HIS 0.003 0.001 HIS E 382 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.13 (20061) covalent geometry : angle 0.53818 / 0.28 (27369) hydrogen bonds : bond 0.04662 / 3.20 ( 1458) hydrogen bonds : angle 4.13439 / 3.02 ( 4257) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5142 Ramachandran restraints generated. 2571 Oldfield, 0 Emsley, 2571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5142 Ramachandran restraints generated. 2571 Oldfield, 0 Emsley, 2571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 2073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 381 time to evaluate : 0.745 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 100 GLU cc_start: 0.8452 (mp0) cc_final: 0.8202 (pm20) REVERT: D 267 MET cc_start: 0.9154 (mmp) cc_final: 0.8712 (mmm) REVERT: D 337 MET cc_start: 0.9375 (tpp) cc_final: 0.8838 (tpt) REVERT: D 451 MET cc_start: 0.9236 (ttp) cc_final: 0.8803 (ttp) REVERT: D 836 MET cc_start: 0.9114 (ptp) cc_final: 0.8911 (ptp) REVERT: G 23 GLU cc_start: 0.8802 (pm20) cc_final: 0.8092 (pm20) REVERT: G 26 GLU cc_start: 0.9039 (tt0) cc_final: 0.8703 (mt-10) REVERT: G 52 GLU cc_start: 0.9078 (tm-30) cc_final: 0.8306 (tm-30) REVERT: G 58 LYS cc_start: 0.8540 (tptt) cc_final: 0.8228 (tptt) REVERT: G 67 LEU cc_start: 0.8118 (mm) cc_final: 0.7816 (mm) REVERT: E 225 TYR cc_start: 0.9043 (m-10) cc_final: 0.8772 (m-10) REVERT: E 337 MET cc_start: 0.9393 (tpp) cc_final: 0.9167 (tpp) REVERT: E 924 ARG cc_start: 0.8770 (OUTLIER) cc_final: 0.8464 (tmm-80) REVERT: F 100 GLU cc_start: 0.8539 (mp0) cc_final: 0.8263 (pm20) REVERT: F 101 GLU cc_start: 0.9020 (mm-30) cc_final: 0.8517 (pm20) REVERT: F 206 MET cc_start: 0.8473 (ttm) cc_final: 0.8175 (tpp) REVERT: F 451 MET cc_start: 0.8999 (ttt) cc_final: 0.8789 (ttt) REVERT: H 23 GLU cc_start: 0.9001 (pm20) cc_final: 0.8328 (pm20) REVERT: H 26 GLU cc_start: 0.9230 (tt0) cc_final: 0.8371 (mt-10) REVERT: H 30 GLU cc_start: 0.8196 (pm20) cc_final: 0.7955 (pm20) REVERT: H 31 LYS cc_start: 0.7999 (mmmm) cc_final: 0.7430 (mmmm) REVERT: H 44 MET cc_start: 0.8881 (mmm) cc_final: 0.8579 (mmm) REVERT: H 54 LYS cc_start: 0.9028 (tptp) cc_final: 0.8718 (tptp) REVERT: H 67 LEU cc_start: 0.8162 (mm) cc_final: 0.7505 (mm) REVERT: H 78 GLN cc_start: 0.9422 (mt0) cc_final: 0.9172 (mt0) REVERT: I 17 GLU cc_start: 0.8699 (tp30) cc_final: 0.8150 (tp30) REVERT: I 23 GLU cc_start: 0.8650 (pm20) cc_final: 0.8408 (pm20) REVERT: I 26 GLU cc_start: 0.8990 (tt0) cc_final: 0.8708 (mt-10) REVERT: I 61 ASP cc_start: 0.7684 (t0) cc_final: 0.7381 (t0) outliers start: 54 outliers final: 39 residues processed: 414 average time/residue: 0.1231 time to fit residues: 81.3494 Evaluate side-chains 403 residues out of total 2073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 363 time to evaluate : 0.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 25 ARG Chi-restraints excluded: chain D residue 37 ILE Chi-restraints excluded: chain D residue 182 SER Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 281 ILE Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain D residue 404 LEU Chi-restraints excluded: chain D residue 816 SER Chi-restraints excluded: chain D residue 921 LEU Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain E residue 25 ARG Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain E residue 198 GLN Chi-restraints excluded: chain E residue 252 LEU Chi-restraints excluded: chain E residue 331 LEU Chi-restraints excluded: chain E residue 353 LEU Chi-restraints excluded: chain E residue 401 VAL Chi-restraints excluded: chain E residue 455 ASP Chi-restraints excluded: chain E residue 483 VAL Chi-restraints excluded: chain E residue 787 ILE Chi-restraints excluded: chain E residue 921 LEU Chi-restraints excluded: chain E residue 924 ARG Chi-restraints excluded: chain E residue 930 SER Chi-restraints excluded: chain F residue 25 ARG Chi-restraints excluded: chain F residue 252 LEU Chi-restraints excluded: chain F residue 281 ILE Chi-restraints excluded: chain F residue 353 LEU Chi-restraints excluded: chain F residue 401 VAL Chi-restraints excluded: chain F residue 404 LEU Chi-restraints excluded: chain F residue 483 VAL Chi-restraints excluded: chain F residue 495 GLU Chi-restraints excluded: chain F residue 787 ILE Chi-restraints excluded: chain F residue 812 LEU Chi-restraints excluded: chain F residue 921 LEU Chi-restraints excluded: chain F residue 930 SER Chi-restraints excluded: chain H residue 59 ILE Chi-restraints excluded: chain H residue 62 GLU Chi-restraints excluded: chain I residue 27 VAL Chi-restraints excluded: chain I residue 62 GLU Chi-restraints excluded: chain I residue 64 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 77 optimal weight: 0.1980 chunk 89 optimal weight: 0.8980 chunk 88 optimal weight: 1.9990 chunk 110 optimal weight: 0.8980 chunk 0 optimal weight: 5.9990 chunk 147 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 230 optimal weight: 4.9990 chunk 243 optimal weight: 6.9990 chunk 94 optimal weight: 3.9990 chunk 236 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 78 GLN E 661 GLN F 430 ASN I 78 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.080590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.068958 restraints weight = 53175.398| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 3.12 r_work: 0.2969 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.2892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 20061 Z= 0.126 Angle : 0.544 8.845 27369 Z= 0.276 Chirality : 0.040 0.198 3276 Planarity : 0.004 0.055 3477 Dihedral : 4.153 40.792 2804 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 2.68 % Allowed : 16.96 % Favored : 80.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: 3.11 (0.17), residues: 2571 helix: 2.47 (0.12), residues: 1752 sheet: 1.73 (0.43), residues: 156 loop : 1.15 (0.25), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 178 TYR 0.033 0.001 TYR H 76 PHE 0.015 0.001 PHE H 33 TRP 0.007 0.001 TRP F 381 HIS 0.003 0.001 HIS E 382 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.13 (20061) covalent geometry : angle 0.54420 / 0.28 (27369) hydrogen bonds : bond 0.04403 / 3.02 ( 1458) hydrogen bonds : angle 4.05985 / 2.96 ( 4257) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5142 Ramachandran restraints generated. 2571 Oldfield, 0 Emsley, 2571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5142 Ramachandran restraints generated. 2571 Oldfield, 0 Emsley, 2571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 2073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 377 time to evaluate : 0.757 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 337 MET cc_start: 0.9373 (tpp) cc_final: 0.8811 (tpt) REVERT: G 23 GLU cc_start: 0.8787 (pm20) cc_final: 0.8026 (pm20) REVERT: G 26 GLU cc_start: 0.9088 (tt0) cc_final: 0.8677 (mt-10) REVERT: G 52 GLU cc_start: 0.9026 (tm-30) cc_final: 0.8404 (tm-30) REVERT: G 58 LYS cc_start: 0.8540 (tptt) cc_final: 0.8211 (tptt) REVERT: G 67 LEU cc_start: 0.8081 (mm) cc_final: 0.7492 (mm) REVERT: E 267 MET cc_start: 0.9008 (mmm) cc_final: 0.8749 (mmm) REVERT: E 337 MET cc_start: 0.9400 (tpp) cc_final: 0.9174 (tpp) REVERT: F 100 GLU cc_start: 0.8569 (mp0) cc_final: 0.8296 (pm20) REVERT: F 101 GLU cc_start: 0.8988 (mm-30) cc_final: 0.8473 (pm20) REVERT: F 788 LEU cc_start: 0.9315 (OUTLIER) cc_final: 0.9094 (tp) REVERT: F 854 LEU cc_start: 0.9407 (tp) cc_final: 0.9169 (tt) REVERT: H 18 GLU cc_start: 0.8909 (tm-30) cc_final: 0.8421 (tm-30) REVERT: H 23 GLU cc_start: 0.8965 (pm20) cc_final: 0.8279 (pm20) REVERT: H 26 GLU cc_start: 0.9192 (tt0) cc_final: 0.8497 (mt-10) REVERT: H 44 MET cc_start: 0.8899 (mmm) cc_final: 0.8648 (mmm) REVERT: H 54 LYS cc_start: 0.9010 (tptp) cc_final: 0.8697 (tptp) REVERT: H 67 LEU cc_start: 0.8177 (mm) cc_final: 0.7648 (mm) REVERT: I 17 GLU cc_start: 0.8701 (tp30) cc_final: 0.8224 (tp30) REVERT: I 23 GLU cc_start: 0.8636 (pm20) cc_final: 0.8343 (pm20) REVERT: I 26 GLU cc_start: 0.8978 (tt0) cc_final: 0.8688 (mt-10) REVERT: I 61 ASP cc_start: 0.7912 (t0) cc_final: 0.7605 (t0) outliers start: 55 outliers final: 42 residues processed: 412 average time/residue: 0.1247 time to fit residues: 81.8176 Evaluate side-chains 405 residues out of total 2073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 362 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 25 ARG Chi-restraints excluded: chain D residue 37 ILE Chi-restraints excluded: chain D residue 214 PHE Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain D residue 404 LEU Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 816 SER Chi-restraints excluded: chain D residue 921 LEU Chi-restraints excluded: chain G residue 62 GLU Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain E residue 25 ARG Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain E residue 198 GLN Chi-restraints excluded: chain E residue 252 LEU Chi-restraints excluded: chain E residue 281 ILE Chi-restraints excluded: chain E residue 331 LEU Chi-restraints excluded: chain E residue 353 LEU Chi-restraints excluded: chain E residue 401 VAL Chi-restraints excluded: chain E residue 455 ASP Chi-restraints excluded: chain E residue 483 VAL Chi-restraints excluded: chain E residue 921 LEU Chi-restraints excluded: chain E residue 930 SER Chi-restraints excluded: chain F residue 25 ARG Chi-restraints excluded: chain F residue 182 SER Chi-restraints excluded: chain F residue 252 LEU Chi-restraints excluded: chain F residue 281 ILE Chi-restraints excluded: chain F residue 353 LEU Chi-restraints excluded: chain F residue 401 VAL Chi-restraints excluded: chain F residue 404 LEU Chi-restraints excluded: chain F residue 483 VAL Chi-restraints excluded: chain F residue 495 GLU Chi-restraints excluded: chain F residue 787 ILE Chi-restraints excluded: chain F residue 788 LEU Chi-restraints excluded: chain F residue 921 LEU Chi-restraints excluded: chain F residue 925 SER Chi-restraints excluded: chain F residue 930 SER Chi-restraints excluded: chain H residue 59 ILE Chi-restraints excluded: chain H residue 62 GLU Chi-restraints excluded: chain I residue 27 VAL Chi-restraints excluded: chain I residue 62 GLU Chi-restraints excluded: chain I residue 64 LEU Chi-restraints excluded: chain I residue 70 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 61 optimal weight: 0.7980 chunk 236 optimal weight: 0.8980 chunk 106 optimal weight: 2.9990 chunk 165 optimal weight: 2.9990 chunk 254 optimal weight: 0.9980 chunk 36 optimal weight: 0.4980 chunk 199 optimal weight: 0.6980 chunk 28 optimal weight: 2.9990 chunk 175 optimal weight: 7.9990 chunk 154 optimal weight: 2.9990 chunk 224 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 680 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 661 GLN H 50 GLN I 78 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.081017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.069380 restraints weight = 53835.555| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 3.13 r_work: 0.2976 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.2974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 20061 Z= 0.125 Angle : 0.556 12.098 27369 Z= 0.281 Chirality : 0.041 0.225 3276 Planarity : 0.004 0.056 3477 Dihedral : 4.112 40.300 2804 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 2.83 % Allowed : 17.25 % Favored : 79.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: 3.11 (0.17), residues: 2571 helix: 2.49 (0.12), residues: 1749 sheet: 1.60 (0.42), residues: 156 loop : 1.14 (0.25), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 924 TYR 0.019 0.001 TYR H 76 PHE 0.021 0.001 PHE E 818 TRP 0.006 0.001 TRP D 825 HIS 0.003 0.001 HIS E 382 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.13 (20061) covalent geometry : angle 0.55591 / 0.28 (27369) hydrogen bonds : bond 0.04282 / 2.93 ( 1458) hydrogen bonds : angle 4.03119 / 2.94 ( 4257) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5142 Ramachandran restraints generated. 2571 Oldfield, 0 Emsley, 2571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5142 Ramachandran restraints generated. 2571 Oldfield, 0 Emsley, 2571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 2073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 372 time to evaluate : 0.746 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 25 ARG cc_start: 0.8575 (OUTLIER) cc_final: 0.7261 (mpp-170) REVERT: D 267 MET cc_start: 0.9137 (mmp) cc_final: 0.8623 (mmm) REVERT: D 337 MET cc_start: 0.9374 (tpp) cc_final: 0.8812 (tpt) REVERT: G 17 GLU cc_start: 0.8853 (tp30) cc_final: 0.8583 (tp30) REVERT: G 23 GLU cc_start: 0.8810 (pm20) cc_final: 0.8148 (pm20) REVERT: G 26 GLU cc_start: 0.9149 (tt0) cc_final: 0.8630 (mt-10) REVERT: G 58 LYS cc_start: 0.8567 (tptt) cc_final: 0.8200 (tptt) REVERT: G 78 GLN cc_start: 0.9257 (mm-40) cc_final: 0.8905 (mm-40) REVERT: E 267 MET cc_start: 0.9036 (mmm) cc_final: 0.8771 (mmm) REVERT: F 37 ILE cc_start: 0.9199 (tp) cc_final: 0.8843 (tp) REVERT: F 94 MET cc_start: 0.8199 (mtp) cc_final: 0.7997 (mtp) REVERT: F 100 GLU cc_start: 0.8547 (mp0) cc_final: 0.8293 (pm20) REVERT: F 101 GLU cc_start: 0.8997 (mm-30) cc_final: 0.8480 (pm20) REVERT: F 173 LYS cc_start: 0.9645 (tppt) cc_final: 0.9305 (ttpp) REVERT: F 206 MET cc_start: 0.8495 (ttm) cc_final: 0.8264 (tpp) REVERT: F 451 MET cc_start: 0.8957 (ttt) cc_final: 0.8715 (ttt) REVERT: F 788 LEU cc_start: 0.9318 (tp) cc_final: 0.9107 (tp) REVERT: H 18 GLU cc_start: 0.8792 (tm-30) cc_final: 0.8367 (tm-30) REVERT: H 23 GLU cc_start: 0.8960 (pm20) cc_final: 0.8256 (pm20) REVERT: H 26 GLU cc_start: 0.9127 (tt0) cc_final: 0.8394 (mt-10) REVERT: H 44 MET cc_start: 0.8938 (mmm) cc_final: 0.8641 (mmm) REVERT: H 54 LYS cc_start: 0.9020 (tptp) cc_final: 0.8704 (tptp) REVERT: H 58 LYS cc_start: 0.8531 (tptt) cc_final: 0.8119 (tptt) REVERT: H 67 LEU cc_start: 0.8143 (mm) cc_final: 0.7626 (mm) REVERT: I 17 GLU cc_start: 0.8745 (tp30) cc_final: 0.8393 (tp30) REVERT: I 23 GLU cc_start: 0.8709 (pm20) cc_final: 0.8374 (pm20) REVERT: I 26 GLU cc_start: 0.8984 (tt0) cc_final: 0.8662 (mt-10) REVERT: I 61 ASP cc_start: 0.7969 (t0) cc_final: 0.7698 (t0) REVERT: I 78 GLN cc_start: 0.9367 (mt0) cc_final: 0.9077 (mm-40) outliers start: 58 outliers final: 48 residues processed: 411 average time/residue: 0.1174 time to fit residues: 77.8016 Evaluate side-chains 411 residues out of total 2073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 362 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 25 ARG Chi-restraints excluded: chain D residue 37 ILE Chi-restraints excluded: chain D residue 182 SER Chi-restraints excluded: chain D residue 214 PHE Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 281 ILE Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain D residue 404 LEU Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 787 ILE Chi-restraints excluded: chain D residue 816 SER Chi-restraints excluded: chain D residue 921 LEU Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain G residue 62 GLU Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain E residue 25 ARG Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain E residue 182 SER Chi-restraints excluded: chain E residue 198 GLN Chi-restraints excluded: chain E residue 231 THR Chi-restraints excluded: chain E residue 252 LEU Chi-restraints excluded: chain E residue 331 LEU Chi-restraints excluded: chain E residue 353 LEU Chi-restraints excluded: chain E residue 401 VAL Chi-restraints excluded: chain E residue 455 ASP Chi-restraints excluded: chain E residue 483 VAL Chi-restraints excluded: chain E residue 787 ILE Chi-restraints excluded: chain E residue 921 LEU Chi-restraints excluded: chain E residue 925 SER Chi-restraints excluded: chain F residue 25 ARG Chi-restraints excluded: chain F residue 182 SER Chi-restraints excluded: chain F residue 239 VAL Chi-restraints excluded: chain F residue 252 LEU Chi-restraints excluded: chain F residue 281 ILE Chi-restraints excluded: chain F residue 353 LEU Chi-restraints excluded: chain F residue 401 VAL Chi-restraints excluded: chain F residue 404 LEU Chi-restraints excluded: chain F residue 483 VAL Chi-restraints excluded: chain F residue 495 GLU Chi-restraints excluded: chain F residue 787 ILE Chi-restraints excluded: chain F residue 921 LEU Chi-restraints excluded: chain F residue 925 SER Chi-restraints excluded: chain H residue 59 ILE Chi-restraints excluded: chain H residue 62 GLU Chi-restraints excluded: chain I residue 27 VAL Chi-restraints excluded: chain I residue 62 GLU Chi-restraints excluded: chain I residue 64 LEU Chi-restraints excluded: chain I residue 70 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 186 optimal weight: 2.9990 chunk 232 optimal weight: 1.9990 chunk 238 optimal weight: 2.9990 chunk 157 optimal weight: 0.0270 chunk 44 optimal weight: 2.9990 chunk 89 optimal weight: 0.0270 chunk 244 optimal weight: 2.9990 chunk 122 optimal weight: 0.0070 chunk 67 optimal weight: 4.9990 chunk 180 optimal weight: 3.9990 chunk 218 optimal weight: 0.0770 overall best weight: 0.4274 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 680 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 661 GLN F 724 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.082360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.070702 restraints weight = 53183.733| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 3.15 r_work: 0.3002 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.3172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 20061 Z= 0.116 Angle : 0.570 13.905 27369 Z= 0.284 Chirality : 0.041 0.245 3276 Planarity : 0.004 0.053 3477 Dihedral : 4.057 39.798 2804 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 2.29 % Allowed : 17.59 % Favored : 80.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: 3.12 (0.17), residues: 2571 helix: 2.51 (0.12), residues: 1746 sheet: 1.61 (0.42), residues: 156 loop : 1.11 (0.25), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 421 TYR 0.024 0.001 TYR H 76 PHE 0.025 0.001 PHE E 437 TRP 0.006 0.001 TRP F 940 HIS 0.004 0.000 HIS D 382 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.12 (20061) covalent geometry : angle 0.56955 / 0.28 (27369) hydrogen bonds : bond 0.03955 / 2.73 ( 1458) hydrogen bonds : angle 3.98094 / 2.90 ( 4257) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5142 Ramachandran restraints generated. 2571 Oldfield, 0 Emsley, 2571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5142 Ramachandran restraints generated. 2571 Oldfield, 0 Emsley, 2571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 2073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 389 time to evaluate : 0.685 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 25 ARG cc_start: 0.8558 (OUTLIER) cc_final: 0.7263 (mpp-170) REVERT: D 267 MET cc_start: 0.9119 (mmp) cc_final: 0.8615 (mmm) REVERT: D 337 MET cc_start: 0.9356 (tpp) cc_final: 0.9092 (tpp) REVERT: D 451 MET cc_start: 0.9196 (ttp) cc_final: 0.8790 (ttp) REVERT: G 23 GLU cc_start: 0.8771 (pm20) cc_final: 0.8048 (pm20) REVERT: G 26 GLU cc_start: 0.9127 (tt0) cc_final: 0.8582 (mt-10) REVERT: G 58 LYS cc_start: 0.8592 (tptt) cc_final: 0.8266 (tptt) REVERT: G 67 LEU cc_start: 0.7908 (mm) cc_final: 0.7323 (mm) REVERT: G 78 GLN cc_start: 0.9306 (mm-40) cc_final: 0.8963 (mm-40) REVERT: E 61 MET cc_start: 0.8874 (ttp) cc_final: 0.8522 (ttp) REVERT: E 267 MET cc_start: 0.9039 (mmm) cc_final: 0.8785 (mmm) REVERT: E 337 MET cc_start: 0.9287 (tpp) cc_final: 0.9076 (tpp) REVERT: F 37 ILE cc_start: 0.9205 (tp) cc_final: 0.8844 (tp) REVERT: F 94 MET cc_start: 0.8201 (mtp) cc_final: 0.7989 (mtp) REVERT: F 100 GLU cc_start: 0.8549 (mp0) cc_final: 0.8308 (pm20) REVERT: F 101 GLU cc_start: 0.8965 (mm-30) cc_final: 0.8445 (pm20) REVERT: F 173 LYS cc_start: 0.9664 (tppt) cc_final: 0.9330 (ttpp) REVERT: F 206 MET cc_start: 0.8446 (ttm) cc_final: 0.8165 (tpp) REVERT: F 788 LEU cc_start: 0.9320 (tp) cc_final: 0.9105 (tp) REVERT: H 18 GLU cc_start: 0.8834 (tm-30) cc_final: 0.8319 (tm-30) REVERT: H 23 GLU cc_start: 0.8979 (pm20) cc_final: 0.8641 (pm20) REVERT: H 26 GLU cc_start: 0.9061 (tt0) cc_final: 0.8640 (tt0) REVERT: H 44 MET cc_start: 0.8930 (mmm) cc_final: 0.8702 (mmm) REVERT: H 54 LYS cc_start: 0.9021 (tptp) cc_final: 0.8575 (tptp) REVERT: H 58 LYS cc_start: 0.8489 (tptt) cc_final: 0.8031 (tptt) REVERT: H 64 LEU cc_start: 0.8928 (OUTLIER) cc_final: 0.8724 (mm) REVERT: H 67 LEU cc_start: 0.7990 (mm) cc_final: 0.7477 (mm) REVERT: I 17 GLU cc_start: 0.8759 (tp30) cc_final: 0.8470 (tp30) REVERT: I 23 GLU cc_start: 0.8701 (pm20) cc_final: 0.8379 (pm20) REVERT: I 26 GLU cc_start: 0.8977 (tt0) cc_final: 0.8660 (mt-10) REVERT: I 61 ASP cc_start: 0.7953 (t0) cc_final: 0.7660 (t0) REVERT: I 78 GLN cc_start: 0.9369 (mt0) cc_final: 0.9104 (mm-40) outliers start: 47 outliers final: 38 residues processed: 418 average time/residue: 0.1230 time to fit residues: 81.7519 Evaluate side-chains 411 residues out of total 2073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 371 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 25 ARG Chi-restraints excluded: chain D residue 37 ILE Chi-restraints excluded: chain D residue 214 PHE Chi-restraints excluded: chain D residue 217 ILE Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 398 CYS Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain D residue 404 LEU Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 816 SER Chi-restraints excluded: chain D residue 921 LEU Chi-restraints excluded: chain G residue 62 GLU Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain E residue 182 SER Chi-restraints excluded: chain E residue 198 GLN Chi-restraints excluded: chain E residue 231 THR Chi-restraints excluded: chain E residue 252 LEU Chi-restraints excluded: chain E residue 353 LEU Chi-restraints excluded: chain E residue 401 VAL Chi-restraints excluded: chain E residue 483 VAL Chi-restraints excluded: chain E residue 680 GLN Chi-restraints excluded: chain E residue 787 ILE Chi-restraints excluded: chain E residue 921 LEU Chi-restraints excluded: chain F residue 25 ARG Chi-restraints excluded: chain F residue 182 SER Chi-restraints excluded: chain F residue 252 LEU Chi-restraints excluded: chain F residue 281 ILE Chi-restraints excluded: chain F residue 353 LEU Chi-restraints excluded: chain F residue 401 VAL Chi-restraints excluded: chain F residue 404 LEU Chi-restraints excluded: chain F residue 483 VAL Chi-restraints excluded: chain F residue 921 LEU Chi-restraints excluded: chain F residue 925 SER Chi-restraints excluded: chain H residue 59 ILE Chi-restraints excluded: chain H residue 62 GLU Chi-restraints excluded: chain H residue 64 LEU Chi-restraints excluded: chain I residue 62 GLU Chi-restraints excluded: chain I residue 64 LEU Chi-restraints excluded: chain I residue 70 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 225 optimal weight: 0.8980 chunk 91 optimal weight: 0.7980 chunk 69 optimal weight: 0.7980 chunk 41 optimal weight: 0.6980 chunk 134 optimal weight: 7.9990 chunk 98 optimal weight: 3.9990 chunk 199 optimal weight: 0.9980 chunk 44 optimal weight: 2.9990 chunk 133 optimal weight: 5.9990 chunk 151 optimal weight: 2.9990 chunk 241 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 680 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 724 HIS E 661 GLN F 82 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.081603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.069947 restraints weight = 52836.286| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 3.15 r_work: 0.2988 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.3220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 20061 Z= 0.130 Angle : 0.583 13.797 27369 Z= 0.292 Chirality : 0.041 0.258 3276 Planarity : 0.004 0.054 3477 Dihedral : 4.025 39.118 2804 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 2.49 % Allowed : 18.27 % Favored : 79.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: 3.21 (0.17), residues: 2571 helix: 2.57 (0.12), residues: 1728 sheet: 1.64 (0.42), residues: 156 loop : 1.21 (0.25), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 421 TYR 0.021 0.001 TYR H 76 PHE 0.027 0.001 PHE E 437 TRP 0.006 0.001 TRP F 954 HIS 0.003 0.001 HIS D 382 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 (20061) covalent geometry : angle 0.58304 / 0.29 (27369) hydrogen bonds : bond 0.04084 / 2.80 ( 1458) hydrogen bonds : angle 3.98223 / 2.91 ( 4257) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5142 Ramachandran restraints generated. 2571 Oldfield, 0 Emsley, 2571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5142 Ramachandran restraints generated. 2571 Oldfield, 0 Emsley, 2571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 2073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 376 time to evaluate : 0.724 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 25 ARG cc_start: 0.8582 (OUTLIER) cc_final: 0.7310 (mpp-170) REVERT: D 66 MET cc_start: 0.9209 (ttp) cc_final: 0.8741 (tmm) REVERT: D 267 MET cc_start: 0.9147 (mmp) cc_final: 0.8636 (mmm) REVERT: D 451 MET cc_start: 0.9222 (ttp) cc_final: 0.8828 (ttp) REVERT: G 23 GLU cc_start: 0.8792 (pm20) cc_final: 0.8278 (pm20) REVERT: G 26 GLU cc_start: 0.9172 (tt0) cc_final: 0.8840 (tt0) REVERT: G 52 GLU cc_start: 0.9097 (tm-30) cc_final: 0.8589 (tm-30) REVERT: G 58 LYS cc_start: 0.8552 (tptt) cc_final: 0.8215 (tptt) REVERT: G 78 GLN cc_start: 0.9302 (mm-40) cc_final: 0.8970 (mm-40) REVERT: E 158 ASP cc_start: 0.8653 (m-30) cc_final: 0.8421 (t0) REVERT: E 337 MET cc_start: 0.9307 (tpp) cc_final: 0.8859 (tpt) REVERT: F 37 ILE cc_start: 0.9216 (tp) cc_final: 0.8858 (tp) REVERT: F 79 ARG cc_start: 0.9261 (tpp-160) cc_final: 0.8967 (tpt90) REVERT: F 94 MET cc_start: 0.8275 (mtp) cc_final: 0.8044 (mtp) REVERT: F 100 GLU cc_start: 0.8559 (mp0) cc_final: 0.8299 (pm20) REVERT: F 101 GLU cc_start: 0.9006 (mm-30) cc_final: 0.8435 (pm20) REVERT: F 173 LYS cc_start: 0.9672 (tppt) cc_final: 0.9339 (ttpp) REVERT: F 206 MET cc_start: 0.8428 (ttm) cc_final: 0.8197 (tpp) REVERT: F 788 LEU cc_start: 0.9322 (tp) cc_final: 0.9110 (tp) REVERT: H 18 GLU cc_start: 0.8812 (tm-30) cc_final: 0.8300 (tm-30) REVERT: H 23 GLU cc_start: 0.8980 (pm20) cc_final: 0.8629 (pm20) REVERT: H 54 LYS cc_start: 0.9022 (tptp) cc_final: 0.8576 (tptp) REVERT: H 58 LYS cc_start: 0.8434 (tptt) cc_final: 0.7977 (tptt) REVERT: H 64 LEU cc_start: 0.8931 (OUTLIER) cc_final: 0.8717 (mm) REVERT: H 67 LEU cc_start: 0.7942 (mm) cc_final: 0.7469 (mm) REVERT: I 17 GLU cc_start: 0.8725 (tp30) cc_final: 0.8446 (tp30) REVERT: I 23 GLU cc_start: 0.8722 (pm20) cc_final: 0.8403 (pm20) REVERT: I 26 GLU cc_start: 0.8971 (tt0) cc_final: 0.8650 (mt-10) REVERT: I 61 ASP cc_start: 0.7922 (t0) cc_final: 0.7626 (t0) REVERT: I 78 GLN cc_start: 0.9345 (mt0) cc_final: 0.9063 (mm-40) outliers start: 51 outliers final: 44 residues processed: 408 average time/residue: 0.1190 time to fit residues: 78.5222 Evaluate side-chains 411 residues out of total 2073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 365 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 25 ARG Chi-restraints excluded: chain D residue 214 PHE Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 281 ILE Chi-restraints excluded: chain D residue 398 CYS Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain D residue 404 LEU Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 787 ILE Chi-restraints excluded: chain D residue 816 SER Chi-restraints excluded: chain D residue 921 LEU Chi-restraints excluded: chain G residue 16 ILE Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain E residue 25 ARG Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain E residue 182 SER Chi-restraints excluded: chain E residue 198 GLN Chi-restraints excluded: chain E residue 231 THR Chi-restraints excluded: chain E residue 239 VAL Chi-restraints excluded: chain E residue 252 LEU Chi-restraints excluded: chain E residue 281 ILE Chi-restraints excluded: chain E residue 353 LEU Chi-restraints excluded: chain E residue 401 VAL Chi-restraints excluded: chain E residue 483 VAL Chi-restraints excluded: chain E residue 680 GLN Chi-restraints excluded: chain E residue 787 ILE Chi-restraints excluded: chain E residue 921 LEU Chi-restraints excluded: chain F residue 25 ARG Chi-restraints excluded: chain F residue 182 SER Chi-restraints excluded: chain F residue 239 VAL Chi-restraints excluded: chain F residue 252 LEU Chi-restraints excluded: chain F residue 281 ILE Chi-restraints excluded: chain F residue 353 LEU Chi-restraints excluded: chain F residue 401 VAL Chi-restraints excluded: chain F residue 404 LEU Chi-restraints excluded: chain F residue 483 VAL Chi-restraints excluded: chain F residue 921 LEU Chi-restraints excluded: chain F residue 925 SER Chi-restraints excluded: chain H residue 59 ILE Chi-restraints excluded: chain H residue 62 GLU Chi-restraints excluded: chain H residue 64 LEU Chi-restraints excluded: chain I residue 62 GLU Chi-restraints excluded: chain I residue 64 LEU Chi-restraints excluded: chain I residue 70 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 9 optimal weight: 0.6980 chunk 21 optimal weight: 0.6980 chunk 231 optimal weight: 4.9990 chunk 233 optimal weight: 2.9990 chunk 149 optimal weight: 0.9990 chunk 102 optimal weight: 0.6980 chunk 74 optimal weight: 6.9990 chunk 148 optimal weight: 1.9990 chunk 152 optimal weight: 5.9990 chunk 15 optimal weight: 0.7980 chunk 164 optimal weight: 0.0870 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 680 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 661 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.082790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.071194 restraints weight = 52975.488| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 3.09 r_work: 0.3004 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.3312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 20061 Z= 0.123 Angle : 0.589 9.851 27369 Z= 0.296 Chirality : 0.041 0.274 3276 Planarity : 0.004 0.054 3477 Dihedral : 4.012 38.844 2804 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 2.29 % Allowed : 18.91 % Favored : 78.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: 3.24 (0.17), residues: 2571 helix: 2.55 (0.12), residues: 1737 sheet: 1.64 (0.42), residues: 156 loop : 1.31 (0.26), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 421 TYR 0.019 0.001 TYR H 76 PHE 0.026 0.001 PHE E 437 TRP 0.006 0.001 TRP F 940 HIS 0.003 0.001 HIS D 382 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 (20061) covalent geometry : angle 0.58927 / 0.30 (27369) hydrogen bonds : bond 0.03987 / 2.74 ( 1458) hydrogen bonds : angle 3.96429 / 2.89 ( 4257) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5142 Ramachandran restraints generated. 2571 Oldfield, 0 Emsley, 2571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5142 Ramachandran restraints generated. 2571 Oldfield, 0 Emsley, 2571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 2073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 375 time to evaluate : 0.583 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 25 ARG cc_start: 0.8545 (OUTLIER) cc_final: 0.7270 (mpp-170) REVERT: D 66 MET cc_start: 0.9186 (ttp) cc_final: 0.8745 (tmm) REVERT: D 173 LYS cc_start: 0.9266 (ttpp) cc_final: 0.9022 (ttpp) REVERT: D 267 MET cc_start: 0.9133 (mmp) cc_final: 0.8618 (mmm) REVERT: D 354 THR cc_start: 0.8749 (m) cc_final: 0.8498 (t) REVERT: D 451 MET cc_start: 0.9218 (ttp) cc_final: 0.8820 (ttp) REVERT: G 23 GLU cc_start: 0.8813 (pm20) cc_final: 0.8083 (pm20) REVERT: G 26 GLU cc_start: 0.9195 (tt0) cc_final: 0.8611 (mt-10) REVERT: G 58 LYS cc_start: 0.8564 (tptt) cc_final: 0.8236 (tptt) REVERT: G 78 GLN cc_start: 0.9295 (mm-40) cc_final: 0.8959 (mm-40) REVERT: E 158 ASP cc_start: 0.8655 (m-30) cc_final: 0.8421 (t0) REVERT: E 337 MET cc_start: 0.9319 (tpp) cc_final: 0.8908 (tpt) REVERT: E 345 MET cc_start: 0.8658 (mmp) cc_final: 0.8441 (mmp) REVERT: F 37 ILE cc_start: 0.9227 (tp) cc_final: 0.8870 (tp) REVERT: F 79 ARG cc_start: 0.9250 (tpp-160) cc_final: 0.8955 (tpt90) REVERT: F 94 MET cc_start: 0.8251 (mtp) cc_final: 0.8024 (mtp) REVERT: F 100 GLU cc_start: 0.8529 (mp0) cc_final: 0.8284 (pm20) REVERT: F 101 GLU cc_start: 0.8990 (mm-30) cc_final: 0.8432 (pm20) REVERT: F 173 LYS cc_start: 0.9665 (tppt) cc_final: 0.9335 (ttpp) REVERT: F 206 MET cc_start: 0.8361 (ttm) cc_final: 0.8128 (tpp) REVERT: F 854 LEU cc_start: 0.9325 (tp) cc_final: 0.8852 (tp) REVERT: H 18 GLU cc_start: 0.8799 (tm-30) cc_final: 0.8307 (tm-30) REVERT: H 23 GLU cc_start: 0.8999 (pm20) cc_final: 0.8668 (pm20) REVERT: H 58 LYS cc_start: 0.8372 (tptt) cc_final: 0.7988 (tptt) REVERT: H 78 GLN cc_start: 0.9182 (mm110) cc_final: 0.8779 (mm-40) REVERT: I 17 GLU cc_start: 0.8749 (tp30) cc_final: 0.8538 (tp30) REVERT: I 23 GLU cc_start: 0.8715 (pm20) cc_final: 0.8384 (pm20) REVERT: I 26 GLU cc_start: 0.8955 (tt0) cc_final: 0.8630 (mt-10) REVERT: I 61 ASP cc_start: 0.7949 (t0) cc_final: 0.7660 (t0) REVERT: I 78 GLN cc_start: 0.9357 (mt0) cc_final: 0.9089 (mm-40) outliers start: 47 outliers final: 42 residues processed: 402 average time/residue: 0.1216 time to fit residues: 78.3400 Evaluate side-chains 415 residues out of total 2073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 372 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 25 ARG Chi-restraints excluded: chain D residue 37 ILE Chi-restraints excluded: chain D residue 214 PHE Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 281 ILE Chi-restraints excluded: chain D residue 398 CYS Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain D residue 404 LEU Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 787 ILE Chi-restraints excluded: chain D residue 816 SER Chi-restraints excluded: chain D residue 921 LEU Chi-restraints excluded: chain G residue 16 ILE Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain E residue 25 ARG Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain E residue 182 SER Chi-restraints excluded: chain E residue 198 GLN Chi-restraints excluded: chain E residue 231 THR Chi-restraints excluded: chain E residue 239 VAL Chi-restraints excluded: chain E residue 252 LEU Chi-restraints excluded: chain E residue 281 ILE Chi-restraints excluded: chain E residue 353 LEU Chi-restraints excluded: chain E residue 401 VAL Chi-restraints excluded: chain E residue 483 VAL Chi-restraints excluded: chain E residue 661 GLN Chi-restraints excluded: chain E residue 787 ILE Chi-restraints excluded: chain E residue 921 LEU Chi-restraints excluded: chain F residue 182 SER Chi-restraints excluded: chain F residue 252 LEU Chi-restraints excluded: chain F residue 281 ILE Chi-restraints excluded: chain F residue 353 LEU Chi-restraints excluded: chain F residue 401 VAL Chi-restraints excluded: chain F residue 404 LEU Chi-restraints excluded: chain F residue 483 VAL Chi-restraints excluded: chain F residue 921 LEU Chi-restraints excluded: chain H residue 59 ILE Chi-restraints excluded: chain H residue 62 GLU Chi-restraints excluded: chain I residue 9 ILE Chi-restraints excluded: chain I residue 62 GLU Chi-restraints excluded: chain I residue 64 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 13 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 chunk 212 optimal weight: 6.9990 chunk 57 optimal weight: 4.9990 chunk 231 optimal weight: 4.9990 chunk 235 optimal weight: 2.9990 chunk 188 optimal weight: 0.9990 chunk 213 optimal weight: 0.9980 chunk 199 optimal weight: 1.9990 chunk 71 optimal weight: 0.8980 chunk 93 optimal weight: 0.6980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 661 GLN ** D 680 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 661 GLN F 680 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.081713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.069858 restraints weight = 53886.747| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 3.24 r_work: 0.2975 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.3292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 20061 Z= 0.145 Angle : 0.608 9.557 27369 Z= 0.304 Chirality : 0.041 0.277 3276 Planarity : 0.004 0.056 3477 Dihedral : 3.959 38.382 2800 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 2.49 % Allowed : 18.71 % Favored : 78.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: 3.26 (0.17), residues: 2571 helix: 2.58 (0.12), residues: 1740 sheet: 1.62 (0.42), residues: 156 loop : 1.29 (0.26), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 62 TYR 0.037 0.001 TYR H 76 PHE 0.025 0.001 PHE E 437 TRP 0.006 0.001 TRP F 954 HIS 0.003 0.001 HIS D 382 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.14 (20061) covalent geometry : angle 0.60755 / 0.30 (27369) hydrogen bonds : bond 0.04195 / 2.88 ( 1458) hydrogen bonds : angle 4.01307 / 2.93 ( 4257) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3951.92 seconds wall clock time: 68 minutes 45.35 seconds (4125.35 seconds total)