Starting phenix.real_space_refine on Thu Feb 5 19:43:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9rgb_53947/02_2026/9rgb_53947.cif Found real_map, /net/cci-nas-00/data/ceres_data/9rgb_53947/02_2026/9rgb_53947.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9rgb_53947/02_2026/9rgb_53947.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9rgb_53947/02_2026/9rgb_53947.map" model { file = "/net/cci-nas-00/data/ceres_data/9rgb_53947/02_2026/9rgb_53947.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9rgb_53947/02_2026/9rgb_53947.cif" } resolution = 3.2 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= 0.000 sd= 0.005 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 6 5.49 5 S 90 5.16 5 C 12563 2.51 5 N 3230 2.21 5 O 3521 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 104 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19410 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 244 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 244 Classifications: {'peptide': 31} Link IDs: {'PTRANS': 1, 'TRANS': 29} Chain: "B" Number of atoms: 244 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 244 Classifications: {'peptide': 31} Link IDs: {'PTRANS': 1, 'TRANS': 29} Chain: "C" Number of atoms: 244 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 244 Classifications: {'peptide': 31} Link IDs: {'PTRANS': 1, 'TRANS': 29} Chain: "D" Number of atoms: 5569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 739, 5569 Classifications: {'peptide': 739} Link IDs: {'PCIS': 1, 'PTRANS': 33, 'TRANS': 704} Chain: "E" Number of atoms: 5569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 739, 5569 Classifications: {'peptide': 739} Link IDs: {'PCIS': 1, 'PTRANS': 33, 'TRANS': 704} Chain: "F" Number of atoms: 5569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 739, 5569 Classifications: {'peptide': 739} Link IDs: {'PCIS': 1, 'PTRANS': 33, 'TRANS': 704} Chain: "G" Number of atoms: 609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 609 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'4HH:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "H" Number of atoms: 614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 614 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 3, 'TRANS': 74} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'4HH:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "I" Number of atoms: 614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 614 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 3, 'TRANS': 74} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'4HH:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'L9Q': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 5 Chain: "B" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 45 Unusual residues: {'L9Q': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Chain: "C" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'L9Q': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Time building chain proxies: 4.65, per 1000 atoms: 0.24 Number of scatterers: 19410 At special positions: 0 Unit cell: (117.465, 127.015, 142.295, 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 90 16.00 P 6 15.00 O 3521 8.00 N 3230 7.00 C 12563 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: 1.90 Conformation dependent library (CDL) restraints added in 984.0 milliseconds 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4648 Finding SS restraints... Secondary structure from input PDB file: 105 helices and 7 sheets defined 71.1% alpha, 5.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.78 Creating SS restraints... Processing helix chain 'A' and resid 2 through 7 Processing helix chain 'A' and resid 8 through 30 removed outlier: 3.808A pdb=" N THR A 30 " --> pdb=" O GLN A 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 8 removed outlier: 3.526A pdb=" N ALA B 8 " --> pdb=" O THR B 4 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 30 removed outlier: 3.817A pdb=" N LEU B 12 " --> pdb=" O ALA B 8 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N THR B 30 " --> pdb=" O GLN B 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 8 removed outlier: 3.770A pdb=" N ALA C 8 " --> pdb=" O THR C 4 " (cutoff:3.500A) Processing helix chain 'C' and resid 8 through 31 removed outlier: 3.534A pdb=" N LEU C 12 " --> pdb=" O ALA C 8 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N THR C 30 " --> pdb=" O GLN C 26 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N PHE C 31 " --> pdb=" O ARG C 27 " (cutoff:3.500A) Processing helix chain 'D' and resid 22 through 31 removed outlier: 3.646A pdb=" N ARG D 26 " --> pdb=" O PRO D 22 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N PHE D 31 " --> pdb=" O MET D 27 " (cutoff:3.500A) Processing helix chain 'D' and resid 31 through 49 removed outlier: 3.529A pdb=" N THR D 49 " --> pdb=" O VAL D 45 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 60 removed outlier: 3.914A pdb=" N GLN D 60 " --> pdb=" O VAL D 56 " (cutoff:3.500A) Processing helix chain 'D' and resid 69 through 82 Processing helix chain 'D' and resid 102 through 119 removed outlier: 3.783A pdb=" N ASP D 119 " --> pdb=" O ARG D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 159 through 175 removed outlier: 3.923A pdb=" N ASN D 163 " --> pdb=" O GLU D 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 189 through 224 removed outlier: 5.645A pdb=" N GLN D 205 " --> pdb=" O ASP D 201 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N VAL D 206 " --> pdb=" O ARG D 202 " (cutoff:3.500A) Processing helix chain 'D' and resid 226 through 253 removed outlier: 3.892A pdb=" N HIS D 253 " --> pdb=" O PHE D 249 " (cutoff:3.500A) Processing helix chain 'D' and resid 259 through 292 removed outlier: 3.525A pdb=" N GLY D 292 " --> pdb=" O ALA D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 294 through 324 removed outlier: 5.883A pdb=" N HIS D 308 " --> pdb=" O GLY D 304 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N VAL D 309 " --> pdb=" O GLY D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 325 through 327 No H-bonds generated for 'chain 'D' and resid 325 through 327' Processing helix chain 'D' and resid 329 through 334 Processing helix chain 'D' and resid 335 through 365 removed outlier: 3.745A pdb=" N LEU D 339 " --> pdb=" O LEU D 335 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N GLY D 354 " --> pdb=" O ALA D 350 " (cutoff:3.500A) Proline residue: D 355 - end of helix removed outlier: 3.743A pdb=" N GLY D 365 " --> pdb=" O THR D 361 " (cutoff:3.500A) Processing helix chain 'D' and resid 374 through 389 removed outlier: 3.719A pdb=" N GLY D 378 " --> pdb=" O ALA D 374 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N TRP D 389 " --> pdb=" O ALA D 385 " (cutoff:3.500A) Processing helix chain 'D' and resid 389 through 406 removed outlier: 3.739A pdb=" N ILE D 393 " --> pdb=" O TRP D 389 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU D 394 " --> pdb=" O PRO D 390 " (cutoff:3.500A) Processing helix chain 'D' and resid 417 through 421 removed outlier: 3.966A pdb=" N LEU D 421 " --> pdb=" O ARG D 418 " (cutoff:3.500A) Processing helix chain 'D' and resid 425 through 438 Processing helix chain 'D' and resid 458 through 474 Processing helix chain 'D' and resid 692 through 697 removed outlier: 3.660A pdb=" N VAL D 695 " --> pdb=" O PRO D 692 " (cutoff:3.500A) Processing helix chain 'D' and resid 698 through 709 Processing helix chain 'D' and resid 728 through 745 removed outlier: 4.256A pdb=" N ILE D 735 " --> pdb=" O GLY D 731 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N ALA D 736 " --> pdb=" O ILE D 732 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N LYS D 737 " --> pdb=" O ALA D 733 " (cutoff:3.500A) Processing helix chain 'D' and resid 761 through 796 Processing helix chain 'D' and resid 797 through 824 removed outlier: 3.872A pdb=" N ALA D 801 " --> pdb=" O SER D 797 " (cutoff:3.500A) Processing helix chain 'D' and resid 834 through 861 Processing helix chain 'D' and resid 865 through 894 removed outlier: 5.077A pdb=" N SER D 879 " --> pdb=" O GLY D 875 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N VAL D 880 " --> pdb=" O GLY D 876 " (cutoff:3.500A) Processing helix chain 'D' and resid 895 through 898 Processing helix chain 'D' and resid 900 through 920 Processing helix chain 'D' and resid 925 through 934 Processing helix chain 'D' and resid 935 through 939 removed outlier: 3.692A pdb=" N TRP D 938 " --> pdb=" O LYS D 935 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N TRP D 939 " --> pdb=" O TRP D 936 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 935 through 939' Processing helix chain 'E' and resid 22 through 31 removed outlier: 3.896A pdb=" N ARG E 26 " --> pdb=" O PRO E 22 " (cutoff:3.500A) Processing helix chain 'E' and resid 31 through 49 Processing helix chain 'E' and resid 52 through 60 Processing helix chain 'E' and resid 69 through 82 Processing helix chain 'E' and resid 102 through 119 removed outlier: 3.638A pdb=" N ASP E 119 " --> pdb=" O ARG E 115 " (cutoff:3.500A) Processing helix chain 'E' and resid 132 through 137 removed outlier: 4.389A pdb=" N THR E 137 " --> pdb=" O PRO E 133 " (cutoff:3.500A) Processing helix chain 'E' and resid 159 through 175 removed outlier: 3.951A pdb=" N ASN E 163 " --> pdb=" O GLU E 159 " (cutoff:3.500A) Processing helix chain 'E' and resid 188 through 203 Processing helix chain 'E' and resid 205 through 224 Processing helix chain 'E' and resid 226 through 253 removed outlier: 3.651A pdb=" N HIS E 253 " --> pdb=" O PHE E 249 " (cutoff:3.500A) Processing helix chain 'E' and resid 259 through 292 removed outlier: 3.858A pdb=" N GLY E 292 " --> pdb=" O ALA E 288 " (cutoff:3.500A) Processing helix chain 'E' and resid 294 through 324 removed outlier: 3.516A pdb=" N TYR E 299 " --> pdb=" O ARG E 295 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N HIS E 308 " --> pdb=" O GLY E 304 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N VAL E 309 " --> pdb=" O GLY E 305 " (cutoff:3.500A) Processing helix chain 'E' and resid 329 through 334 removed outlier: 3.846A pdb=" N THR E 334 " --> pdb=" O PRO E 330 " (cutoff:3.500A) Processing helix chain 'E' and resid 335 through 365 removed outlier: 4.235A pdb=" N GLY E 354 " --> pdb=" O ALA E 350 " (cutoff:3.500A) Proline residue: E 355 - end of helix removed outlier: 4.185A pdb=" N GLY E 365 " --> pdb=" O THR E 361 " (cutoff:3.500A) Processing helix chain 'E' and resid 374 through 389 removed outlier: 3.505A pdb=" N ARG E 388 " --> pdb=" O ALA E 384 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N TRP E 389 " --> pdb=" O ALA E 385 " (cutoff:3.500A) Processing helix chain 'E' and resid 389 through 406 removed outlier: 3.663A pdb=" N ILE E 393 " --> pdb=" O TRP E 389 " (cutoff:3.500A) Processing helix chain 'E' and resid 417 through 421 removed outlier: 3.637A pdb=" N TYR E 420 " --> pdb=" O ASP E 417 " (cutoff:3.500A) Processing helix chain 'E' and resid 425 through 438 removed outlier: 3.988A pdb=" N HIS E 437 " --> pdb=" O ALA E 433 " (cutoff:3.500A) Processing helix chain 'E' and resid 458 through 474 Processing helix chain 'E' and resid 692 through 697 removed outlier: 3.649A pdb=" N VAL E 695 " --> pdb=" O PRO E 692 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N PHE E 696 " --> pdb=" O PRO E 693 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ASP E 697 " --> pdb=" O GLU E 694 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 692 through 697' Processing helix chain 'E' and resid 698 through 709 Processing helix chain 'E' and resid 728 through 746 removed outlier: 4.175A pdb=" N ILE E 735 " --> pdb=" O GLY E 731 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N ALA E 736 " --> pdb=" O ILE E 732 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N LYS E 737 " --> pdb=" O ALA E 733 " (cutoff:3.500A) Processing helix chain 'E' and resid 761 through 796 Processing helix chain 'E' and resid 797 through 825 removed outlier: 3.558A pdb=" N ALA E 801 " --> pdb=" O SER E 797 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N HIS E 825 " --> pdb=" O LEU E 821 " (cutoff:3.500A) Processing helix chain 'E' and resid 833 through 861 removed outlier: 3.764A pdb=" N GLU E 861 " --> pdb=" O ARG E 857 " (cutoff:3.500A) Processing helix chain 'E' and resid 866 through 894 removed outlier: 5.385A pdb=" N SER E 879 " --> pdb=" O GLY E 875 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N VAL E 880 " --> pdb=" O GLY E 876 " (cutoff:3.500A) Processing helix chain 'E' and resid 895 through 898 Processing helix chain 'E' and resid 900 through 920 Processing helix chain 'E' and resid 920 through 925 Processing helix chain 'E' and resid 925 through 934 Processing helix chain 'E' and resid 935 through 938 removed outlier: 3.844A pdb=" N TRP E 938 " --> pdb=" O LYS E 935 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 935 through 938' Processing helix chain 'F' and resid 22 through 31 Processing helix chain 'F' and resid 31 through 50 removed outlier: 3.894A pdb=" N THR F 49 " --> pdb=" O VAL F 45 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N VAL F 50 " --> pdb=" O LEU F 46 " (cutoff:3.500A) Processing helix chain 'F' and resid 52 through 60 Processing helix chain 'F' and resid 69 through 82 Processing helix chain 'F' and resid 102 through 119 removed outlier: 3.798A pdb=" N ASP F 119 " --> pdb=" O ARG F 115 " (cutoff:3.500A) Processing helix chain 'F' and resid 159 through 174 removed outlier: 3.647A pdb=" N ASN F 163 " --> pdb=" O GLU F 159 " (cutoff:3.500A) Processing helix chain 'F' and resid 188 through 200 Processing helix chain 'F' and resid 204 through 223 Processing helix chain 'F' and resid 225 through 253 removed outlier: 3.597A pdb=" N SER F 229 " --> pdb=" O SER F 225 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N HIS F 253 " --> pdb=" O PHE F 249 " (cutoff:3.500A) Processing helix chain 'F' and resid 259 through 291 Processing helix chain 'F' and resid 296 through 324 removed outlier: 3.820A pdb=" N TYR F 300 " --> pdb=" O GLU F 296 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N HIS F 308 " --> pdb=" O GLY F 304 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N VAL F 309 " --> pdb=" O GLY F 305 " (cutoff:3.500A) Processing helix chain 'F' and resid 329 through 334 Processing helix chain 'F' and resid 335 through 365 removed outlier: 3.975A pdb=" N LEU F 339 " --> pdb=" O LEU F 335 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N GLY F 354 " --> pdb=" O ALA F 350 " (cutoff:3.500A) Proline residue: F 355 - end of helix removed outlier: 3.611A pdb=" N ARG F 363 " --> pdb=" O ALA F 359 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N GLY F 365 " --> pdb=" O THR F 361 " (cutoff:3.500A) Processing helix chain 'F' and resid 374 through 389 Processing helix chain 'F' and resid 389 through 406 removed outlier: 3.645A pdb=" N ILE F 393 " --> pdb=" O TRP F 389 " (cutoff:3.500A) Processing helix chain 'F' and resid 417 through 421 removed outlier: 3.536A pdb=" N LEU F 421 " --> pdb=" O ARG F 418 " (cutoff:3.500A) Processing helix chain 'F' and resid 425 through 438 Processing helix chain 'F' and resid 458 through 474 removed outlier: 3.570A pdb=" N PHE F 462 " --> pdb=" O ASN F 458 " (cutoff:3.500A) Processing helix chain 'F' and resid 692 through 697 removed outlier: 3.541A pdb=" N VAL F 695 " --> pdb=" O PRO F 692 " (cutoff:3.500A) Processing helix chain 'F' and resid 698 through 709 removed outlier: 3.707A pdb=" N GLN F 702 " --> pdb=" O ASN F 698 " (cutoff:3.500A) Processing helix chain 'F' and resid 728 through 733 removed outlier: 3.884A pdb=" N ALA F 733 " --> pdb=" O GLN F 729 " (cutoff:3.500A) Processing helix chain 'F' and resid 734 through 746 Processing helix chain 'F' and resid 761 through 796 Processing helix chain 'F' and resid 797 through 824 removed outlier: 3.830A pdb=" N ALA F 801 " --> pdb=" O SER F 797 " (cutoff:3.500A) Processing helix chain 'F' and resid 832 through 861 removed outlier: 3.613A pdb=" N LEU F 836 " --> pdb=" O HIS F 832 " (cutoff:3.500A) Processing helix chain 'F' and resid 865 through 894 removed outlier: 5.110A pdb=" N SER F 879 " --> pdb=" O GLY F 875 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N VAL F 880 " --> pdb=" O GLY F 876 " (cutoff:3.500A) Processing helix chain 'F' and resid 895 through 898 Processing helix chain 'F' and resid 900 through 920 Processing helix chain 'F' and resid 920 through 934 removed outlier: 4.733A pdb=" N THR F 926 " --> pdb=" O ARG F 922 " (cutoff:3.500A) Proline residue: F 927 - end of helix Processing helix chain 'F' and resid 935 through 939 removed outlier: 3.546A pdb=" N TRP F 938 " --> pdb=" O LYS F 935 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N TRP F 939 " --> pdb=" O TRP F 936 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 935 through 939' Processing helix chain 'G' and resid 5 through 20 Processing helix chain 'G' and resid 40 through 56 Processing helix chain 'G' and resid 69 through 80 removed outlier: 3.572A pdb=" N LEU G 80 " --> pdb=" O TYR G 76 " (cutoff:3.500A) Processing helix chain 'H' and resid 4 through 21 Processing helix chain 'H' and resid 40 through 55 removed outlier: 4.031A pdb=" N GLU H 46 " --> pdb=" O LEU H 42 " (cutoff:3.500A) Processing helix chain 'H' and resid 69 through 80 Processing helix chain 'I' and resid 4 through 21 Processing helix chain 'I' and resid 40 through 55 Processing helix chain 'I' and resid 69 through 79 Processing sheet with id=AA1, first strand: chain 'D' and resid 123 through 127 removed outlier: 3.963A pdb=" N GLN D 150 " --> pdb=" O GLN D 127 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 413 through 414 Processing sheet with id=AA3, first strand: chain 'D' and resid 478 through 482 Processing sheet with id=AA4, first strand: chain 'E' and resid 123 through 127 removed outlier: 4.127A pdb=" N GLN E 150 " --> pdb=" O GLN E 127 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 478 through 482 Processing sheet with id=AA6, first strand: chain 'F' and resid 123 through 127 removed outlier: 4.588A pdb=" N GLN F 150 " --> pdb=" O GLN F 127 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 478 through 482 1389 hydrogen bonds defined for protein. 4119 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: 3.65 Time building geometry restraints manager: 2.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3141 1.31 - 1.44: 4894 1.44 - 1.56: 11561 1.56 - 1.69: 9 1.69 - 1.82: 171 Bond restraints: 19776 Sorted by residual: bond pdb=" OG 4HH H 41 " pdb=" P 4HH H 41 " ideal model delta sigma weight residual 1.624 1.493 0.131 2.00e-02 2.50e+03 4.26e+01 bond pdb=" OG 4HH G 41 " pdb=" P 4HH G 41 " ideal model delta sigma weight residual 1.624 1.507 0.117 2.00e-02 2.50e+03 3.40e+01 bond pdb=" OG 4HH I 41 " pdb=" P 4HH I 41 " ideal model delta sigma weight residual 1.624 1.510 0.114 2.00e-02 2.50e+03 3.26e+01 bond pdb=" CQ 4HH G 41 " pdb=" NR 4HH G 41 " ideal model delta sigma weight residual 1.374 1.451 -0.077 2.00e-02 2.50e+03 1.47e+01 bond pdb=" CQ 4HH I 41 " pdb=" NR 4HH I 41 " ideal model delta sigma weight residual 1.374 1.450 -0.076 2.00e-02 2.50e+03 1.43e+01 ... (remaining 19771 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.81: 26773 4.81 - 9.62: 105 9.62 - 14.43: 13 14.43 - 19.23: 0 19.23 - 24.04: 2 Bond angle restraints: 26893 Sorted by residual: angle pdb=" CB 4HH H 41 " pdb=" OG 4HH H 41 " pdb=" P 4HH H 41 " ideal model delta sigma weight residual 119.19 143.23 -24.04 3.00e+00 1.11e-01 6.42e+01 angle pdb=" CB 4HH I 41 " pdb=" OG 4HH I 41 " pdb=" P 4HH I 41 " ideal model delta sigma weight residual 119.19 96.69 22.50 3.00e+00 1.11e-01 5.63e+01 angle pdb=" O1P 4HH H 41 " pdb=" P 4HH H 41 " pdb=" O2P 4HH H 41 " ideal model delta sigma weight residual 122.75 109.22 13.53 3.00e+00 1.11e-01 2.03e+01 angle pdb=" O1P 4HH G 41 " pdb=" P 4HH G 41 " pdb=" O2P 4HH G 41 " ideal model delta sigma weight residual 122.75 109.72 13.03 3.00e+00 1.11e-01 1.89e+01 angle pdb=" O1P 4HH I 41 " pdb=" P 4HH I 41 " pdb=" O2P 4HH I 41 " ideal model delta sigma weight residual 122.75 109.79 12.96 3.00e+00 1.11e-01 1.87e+01 ... (remaining 26888 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.90: 11285 29.90 - 59.81: 442 59.81 - 89.71: 44 89.71 - 119.61: 4 119.61 - 149.51: 2 Dihedral angle restraints: 11777 sinusoidal: 4538 harmonic: 7239 Sorted by residual: dihedral pdb=" CA ILE F 862 " pdb=" C ILE F 862 " pdb=" N HIS F 863 " pdb=" CA HIS F 863 " ideal model delta harmonic sigma weight residual -180.00 -154.39 -25.61 0 5.00e+00 4.00e-02 2.62e+01 dihedral pdb=" CA ASN F 867 " pdb=" C ASN F 867 " pdb=" N THR F 868 " pdb=" CA THR F 868 " ideal model delta harmonic sigma weight residual 180.00 155.95 24.05 0 5.00e+00 4.00e-02 2.31e+01 dihedral pdb=" CA ASN D 867 " pdb=" C ASN D 867 " pdb=" N THR D 868 " pdb=" CA THR D 868 " ideal model delta harmonic sigma weight residual 180.00 157.01 22.99 0 5.00e+00 4.00e-02 2.11e+01 ... (remaining 11774 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 2555 0.064 - 0.128: 613 0.128 - 0.192: 53 0.192 - 0.256: 4 0.256 - 0.320: 2 Chirality restraints: 3227 Sorted by residual: chirality pdb=" CB ILE I 59 " pdb=" CA ILE I 59 " pdb=" CG1 ILE I 59 " pdb=" CG2 ILE I 59 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.32 2.00e-01 2.50e+01 2.56e+00 chirality pdb=" CG LEU F 853 " pdb=" CB LEU F 853 " pdb=" CD1 LEU F 853 " pdb=" CD2 LEU F 853 " both_signs ideal model delta sigma weight residual False -2.59 -2.30 -0.29 2.00e-01 2.50e+01 2.10e+00 chirality pdb=" CG LEU F 367 " pdb=" CB LEU F 367 " pdb=" CD1 LEU F 367 " pdb=" CD2 LEU F 367 " both_signs ideal model delta sigma weight residual False -2.59 -2.37 -0.22 2.00e-01 2.50e+01 1.21e+00 ... (remaining 3224 not shown) Planarity restraints: 3377 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE F 280 " 0.014 2.00e-02 2.50e+03 2.87e-02 1.45e+01 pdb=" CG PHE F 280 " -0.063 2.00e-02 2.50e+03 pdb=" CD1 PHE F 280 " 0.033 2.00e-02 2.50e+03 pdb=" CD2 PHE F 280 " 0.022 2.00e-02 2.50e+03 pdb=" CE1 PHE F 280 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 PHE F 280 " 0.004 2.00e-02 2.50e+03 pdb=" CZ PHE F 280 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 280 " -0.018 2.00e-02 2.50e+03 2.36e-02 9.78e+00 pdb=" CG PHE D 280 " 0.054 2.00e-02 2.50e+03 pdb=" CD1 PHE D 280 " -0.020 2.00e-02 2.50e+03 pdb=" CD2 PHE D 280 " -0.016 2.00e-02 2.50e+03 pdb=" CE1 PHE D 280 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE D 280 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE D 280 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS D 490 " -0.045 5.00e-02 4.00e+02 6.78e-02 7.35e+00 pdb=" N PRO D 491 " 0.117 5.00e-02 4.00e+02 pdb=" CA PRO D 491 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO D 491 " -0.039 5.00e-02 4.00e+02 ... (remaining 3374 not shown) Histogram of nonbonded interaction distances: 2.45 - 2.94: 7527 2.94 - 3.43: 20552 3.43 - 3.92: 30862 3.92 - 4.41: 33563 4.41 - 4.90: 58634 Nonbonded interactions: 151138 Sorted by model distance: nonbonded pdb=" O2 L9Q B 201 " pdb=" O3 L9Q B 201 " model vdw 2.446 2.432 nonbonded pdb=" O2 L9Q A 201 " pdb=" O3 L9Q A 201 " model vdw 2.573 2.432 nonbonded pdb=" CB 4HH I 41 " pdb=" O1P 4HH I 41 " model vdw 2.591 2.752 nonbonded pdb=" CM 4HH G 41 " pdb=" O3P 4HH G 41 " model vdw 2.593 2.776 nonbonded pdb=" O ASN F 466 " pdb=" ND2 ASN F 466 " model vdw 2.599 3.120 ... (remaining 151133 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 31 or (resid 201 and (name N or name C1 or name \ C11 or name C12 or name C13 or name C14 or name C15 or name C16 or name C17 or n \ ame C18 or name C19 or name C2 or name C20 or name C3 or name C31 or name C32 or \ name C33 or name C34 or name C35 or name C36 or name C37 or name C38 or name C3 \ 9 or name C4 or name C40 or name C41 or name C42 or name C5 or name O11 or name \ O1P or name O2 or name O2P or name O3 or name O31 or name O3P or name O4P or nam \ e P )))) selection = (chain 'B' and (resid 1 through 31 or (resid 201 and (name N or name C1 or name \ C11 or name C12 or name C13 or name C14 or name C15 or name C16 or name C17 or n \ ame C18 or name C19 or name C2 or name C20 or name C3 or name C31 or name C32 or \ name C33 or name C34 or name C35 or name C36 or name C37 or name C38 or name C3 \ 9 or name C4 or name C40 or name C41 or name C42 or name C5 or name O11 or name \ O1P or name O2 or name O2P or name O3 or name O31 or name O3P or name O4P or nam \ e P )))) selection = (chain 'C' and (resid 1 through 31 or (resid 201 and (name N or name C1 or name \ C11 or name C12 or name C13 or name C14 or name C15 or name C16 or name C17 or n \ ame C18 or name C19 or name C2 or name C20 or name C3 or name C31 or name C32 or \ name C33 or name C34 or name C35 or name C36 or name C37 or name C38 or name C3 \ 9 or name C4 or name C40 or name C41 or name C42 or name C5 or name O11 or name \ O1P or name O2 or name O2P or name O3 or name O31 or name O3P or name O4P or nam \ e P )))) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = (chain 'H' and resid 4 through 80) selection = (chain 'I' and resid 4 through 80) } 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: 4.190 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: 0.230 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 19.010 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 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 : 0.005 0.131 19776 Z= 0.256 Angle : 0.961 24.043 26893 Z= 0.474 Chirality : 0.052 0.320 3227 Planarity : 0.007 0.069 3377 Dihedral : 15.282 149.513 7129 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.91 % Favored : 98.05 % Rotamer: Outliers : 0.20 % Allowed : 2.43 % Favored : 97.37 % 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: -0.34 (0.16), residues: 2516 helix: 0.04 (0.11), residues: 1690 sheet: 1.77 (0.46), residues: 159 loop : -1.15 (0.23), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG F 224 TYR 0.027 0.002 TYR F 774 PHE 0.063 0.002 PHE F 280 TRP 0.025 0.002 TRP E 833 HIS 0.012 0.001 HIS F 308 Details of bonding type rmsd covalent geometry : bond 0.00537 (19776) covalent geometry : angle 0.96142 (26893) hydrogen bonds : bond 0.11826 ( 1389) hydrogen bonds : angle 5.75796 ( 4119) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 408 time to evaluate : 0.727 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: B 7 ARG cc_start: 0.8350 (mtt180) cc_final: 0.8049 (mmm160) REVERT: C 7 ARG cc_start: 0.8150 (tmm160) cc_final: 0.7487 (mtt180) REVERT: D 27 MET cc_start: 0.7708 (tpp) cc_final: 0.7413 (tpp) REVERT: D 327 THR cc_start: 0.7910 (m) cc_final: 0.7683 (m) REVERT: D 417 ASP cc_start: 0.8315 (p0) cc_final: 0.7876 (p0) REVERT: E 266 LEU cc_start: 0.8762 (tt) cc_final: 0.8448 (tp) REVERT: E 357 ILE cc_start: 0.8605 (pt) cc_final: 0.8361 (pt) REVERT: F 235 MET cc_start: 0.7964 (mtt) cc_final: 0.7439 (mtt) outliers start: 4 outliers final: 0 residues processed: 411 average time/residue: 0.1326 time to fit residues: 86.5312 Evaluate side-chains 292 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 292 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 216 optimal weight: 0.0060 chunk 98 optimal weight: 0.7980 chunk 194 optimal weight: 0.8980 chunk 227 optimal weight: 0.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 247 optimal weight: 2.9990 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 0.8980 overall best weight: 0.6796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 26 GLN ** D 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 444 ASN D 722 HIS E 150 GLN E 440 GLN E 729 GLN F 111 GLN F 117 GLN F 150 GLN F 440 GLN ** F 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 50 GLN ** I 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.101606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.085854 restraints weight = 48685.521| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 2.93 r_work: 0.3311 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.1273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 19776 Z= 0.130 Angle : 0.601 11.246 26893 Z= 0.307 Chirality : 0.042 0.219 3227 Planarity : 0.005 0.047 3377 Dihedral : 8.403 153.614 2845 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.71 % Favored : 98.25 % Rotamer: Outliers : 1.78 % Allowed : 10.35 % Favored : 87.87 % 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: 0.99 (0.16), residues: 2516 helix: 1.20 (0.12), residues: 1690 sheet: 1.82 (0.45), residues: 159 loop : -0.95 (0.23), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 418 TYR 0.021 0.001 TYR E 850 PHE 0.048 0.001 PHE D 280 TRP 0.016 0.001 TRP E 833 HIS 0.006 0.001 HIS D 122 Details of bonding type rmsd covalent geometry : bond 0.00277 (19776) covalent geometry : angle 0.60079 (26893) hydrogen bonds : bond 0.04805 ( 1389) hydrogen bonds : angle 4.47704 ( 4119) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 308 time to evaluate : 0.550 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: B 7 ARG cc_start: 0.8266 (mtt180) cc_final: 0.7768 (mmm160) REVERT: C 7 ARG cc_start: 0.8041 (tmm160) cc_final: 0.7166 (mtt180) REVERT: D 27 MET cc_start: 0.7782 (tpp) cc_final: 0.7567 (tpp) REVERT: D 58 GLN cc_start: 0.8903 (mp10) cc_final: 0.8675 (mp10) REVERT: D 59 ILE cc_start: 0.8491 (mm) cc_final: 0.8222 (mm) REVERT: D 351 LEU cc_start: 0.8453 (OUTLIER) cc_final: 0.8184 (mm) REVERT: D 417 ASP cc_start: 0.8818 (p0) cc_final: 0.8352 (p0) REVERT: D 815 SER cc_start: 0.8460 (t) cc_final: 0.8038 (m) REVERT: D 838 MET cc_start: 0.7775 (mtm) cc_final: 0.7555 (mmp) REVERT: E 233 LEU cc_start: 0.8888 (mt) cc_final: 0.8641 (mt) REVERT: E 357 ILE cc_start: 0.8247 (pt) cc_final: 0.8033 (pt) REVERT: F 443 MET cc_start: 0.9080 (mmp) cc_final: 0.8754 (mmp) REVERT: I 17 GLU cc_start: 0.8277 (tp30) cc_final: 0.7539 (tp30) outliers start: 36 outliers final: 16 residues processed: 332 average time/residue: 0.1208 time to fit residues: 65.7699 Evaluate side-chains 291 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 274 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain D residue 106 HIS Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 260 THR Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 351 LEU Chi-restraints excluded: chain D residue 738 ILE Chi-restraints excluded: chain E residue 201 ASP Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 111 GLN Chi-restraints excluded: chain F residue 174 GLU Chi-restraints excluded: chain F residue 243 THR Chi-restraints excluded: chain F residue 260 THR Chi-restraints excluded: chain F residue 353 LEU Chi-restraints excluded: chain F residue 833 TRP Chi-restraints excluded: chain G residue 26 GLU Chi-restraints excluded: chain I residue 28 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 26 optimal weight: 4.9990 chunk 38 optimal weight: 0.7980 chunk 228 optimal weight: 0.9980 chunk 161 optimal weight: 0.8980 chunk 22 optimal weight: 4.9990 chunk 79 optimal weight: 3.9990 chunk 76 optimal weight: 0.7980 chunk 233 optimal weight: 2.9990 chunk 133 optimal weight: 1.9990 chunk 217 optimal weight: 0.7980 chunk 110 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 941 GLN ** E 428 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 440 GLN E 729 GLN F 111 GLN F 333 GLN ** F 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 50 GLN ** I 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.102434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.086769 restraints weight = 48408.940| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 2.76 r_work: 0.3353 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.1574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 19776 Z= 0.128 Angle : 0.564 9.794 26893 Z= 0.290 Chirality : 0.042 0.263 3227 Planarity : 0.004 0.041 3377 Dihedral : 8.152 153.374 2845 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.75 % Favored : 98.21 % Rotamer: Outliers : 1.58 % Allowed : 12.93 % Favored : 85.49 % 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: 1.43 (0.17), residues: 2516 helix: 1.59 (0.12), residues: 1686 sheet: 1.74 (0.45), residues: 159 loop : -0.88 (0.23), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 224 TYR 0.016 0.001 TYR E 850 PHE 0.035 0.001 PHE D 280 TRP 0.015 0.001 TRP F 833 HIS 0.004 0.001 HIS D 122 Details of bonding type rmsd covalent geometry : bond 0.00282 (19776) covalent geometry : angle 0.56412 (26893) hydrogen bonds : bond 0.04440 ( 1389) hydrogen bonds : angle 4.27242 ( 4119) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 297 time to evaluate : 0.777 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: B 7 ARG cc_start: 0.8215 (mtt180) cc_final: 0.7839 (mmm160) REVERT: C 7 ARG cc_start: 0.8129 (tmm160) cc_final: 0.7313 (mtt180) REVERT: D 58 GLN cc_start: 0.8862 (mp10) cc_final: 0.8503 (mp10) REVERT: D 59 ILE cc_start: 0.8479 (mm) cc_final: 0.8255 (mm) REVERT: D 113 ILE cc_start: 0.8457 (OUTLIER) cc_final: 0.8222 (tp) REVERT: D 327 THR cc_start: 0.6968 (m) cc_final: 0.6746 (m) REVERT: D 351 LEU cc_start: 0.8417 (OUTLIER) cc_final: 0.8146 (mm) REVERT: D 417 ASP cc_start: 0.8711 (p0) cc_final: 0.8242 (p0) REVERT: D 815 SER cc_start: 0.8638 (t) cc_final: 0.8206 (m) REVERT: E 233 LEU cc_start: 0.8787 (mt) cc_final: 0.8554 (mt) REVERT: E 357 ILE cc_start: 0.8263 (pt) cc_final: 0.8058 (pt) outliers start: 32 outliers final: 20 residues processed: 316 average time/residue: 0.1232 time to fit residues: 64.0034 Evaluate side-chains 301 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 279 time to evaluate : 0.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ILE Chi-restraints excluded: chain D residue 113 ILE Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 260 THR Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 351 LEU Chi-restraints excluded: chain D residue 738 ILE Chi-restraints excluded: chain D residue 858 LEU Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 201 ASP Chi-restraints excluded: chain E residue 744 GLU Chi-restraints excluded: chain E residue 777 MET Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 124 GLN Chi-restraints excluded: chain F residue 174 GLU Chi-restraints excluded: chain F residue 243 THR Chi-restraints excluded: chain F residue 260 THR Chi-restraints excluded: chain F residue 353 LEU Chi-restraints excluded: chain F residue 833 TRP Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain I residue 28 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 51 optimal weight: 0.6980 chunk 215 optimal weight: 0.9980 chunk 229 optimal weight: 0.0770 chunk 36 optimal weight: 10.0000 chunk 14 optimal weight: 1.9990 chunk 3 optimal weight: 7.9990 chunk 68 optimal weight: 1.9990 chunk 91 optimal weight: 5.9990 chunk 17 optimal weight: 8.9990 chunk 6 optimal weight: 10.0000 chunk 226 optimal weight: 1.9990 overall best weight: 1.1542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 157 GLN ** E 428 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 440 GLN E 729 GLN F 111 GLN F 440 GLN ** F 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 78 GLN ** H 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.101334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.085607 restraints weight = 48785.223| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 2.76 r_work: 0.3332 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.1836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 19776 Z= 0.140 Angle : 0.571 9.352 26893 Z= 0.292 Chirality : 0.042 0.268 3227 Planarity : 0.004 0.043 3377 Dihedral : 8.049 154.258 2845 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.91 % Favored : 98.05 % Rotamer: Outliers : 2.38 % Allowed : 14.07 % Favored : 83.56 % 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: 1.64 (0.17), residues: 2516 helix: 1.72 (0.12), residues: 1710 sheet: 1.59 (0.45), residues: 162 loop : -0.75 (0.24), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 68 TYR 0.012 0.001 TYR E 850 PHE 0.054 0.001 PHE D 280 TRP 0.016 0.001 TRP F 833 HIS 0.003 0.001 HIS D 122 Details of bonding type rmsd covalent geometry : bond 0.00316 (19776) covalent geometry : angle 0.57087 (26893) hydrogen bonds : bond 0.04397 ( 1389) hydrogen bonds : angle 4.18496 ( 4119) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 290 time to evaluate : 0.830 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: B 7 ARG cc_start: 0.8254 (mtt180) cc_final: 0.7851 (mmm160) REVERT: B 27 ARG cc_start: 0.7647 (ttm-80) cc_final: 0.6628 (ttt180) REVERT: C 7 ARG cc_start: 0.8134 (tmm160) cc_final: 0.7297 (mtt180) REVERT: D 59 ILE cc_start: 0.8501 (mm) cc_final: 0.8299 (mm) REVERT: D 113 ILE cc_start: 0.8508 (OUTLIER) cc_final: 0.8203 (tp) REVERT: D 157 GLN cc_start: 0.7361 (OUTLIER) cc_final: 0.7151 (mp-120) REVERT: D 351 LEU cc_start: 0.8423 (OUTLIER) cc_final: 0.8147 (mm) REVERT: D 417 ASP cc_start: 0.8707 (p0) cc_final: 0.8217 (p0) REVERT: D 815 SER cc_start: 0.8589 (t) cc_final: 0.8162 (m) REVERT: E 153 LEU cc_start: 0.8459 (OUTLIER) cc_final: 0.8116 (mt) REVERT: E 233 LEU cc_start: 0.8792 (mt) cc_final: 0.8581 (mt) REVERT: G 17 GLU cc_start: 0.8105 (tp30) cc_final: 0.7868 (tp30) outliers start: 48 outliers final: 29 residues processed: 316 average time/residue: 0.1234 time to fit residues: 63.8775 Evaluate side-chains 298 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 265 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ILE Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain D residue 113 ILE Chi-restraints excluded: chain D residue 157 GLN Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 260 THR Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 351 LEU Chi-restraints excluded: chain D residue 738 ILE Chi-restraints excluded: chain D residue 776 LEU Chi-restraints excluded: chain D residue 858 LEU Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 164 GLU Chi-restraints excluded: chain E residue 201 ASP Chi-restraints excluded: chain E residue 234 THR Chi-restraints excluded: chain E residue 744 GLU Chi-restraints excluded: chain E residue 777 MET Chi-restraints excluded: chain E residue 903 MET Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 142 SER Chi-restraints excluded: chain F residue 174 GLU Chi-restraints excluded: chain F residue 243 THR Chi-restraints excluded: chain F residue 260 THR Chi-restraints excluded: chain F residue 353 LEU Chi-restraints excluded: chain F residue 833 TRP Chi-restraints excluded: chain G residue 26 GLU Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain I residue 28 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 211 optimal weight: 0.9980 chunk 39 optimal weight: 0.4980 chunk 65 optimal weight: 0.8980 chunk 37 optimal weight: 0.8980 chunk 60 optimal weight: 0.8980 chunk 169 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 212 optimal weight: 0.7980 chunk 6 optimal weight: 10.0000 chunk 28 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 157 GLN E 428 ASN E 440 GLN ** F 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.101875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.086216 restraints weight = 48310.084| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 2.77 r_work: 0.3342 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.1976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 19776 Z= 0.123 Angle : 0.558 10.356 26893 Z= 0.283 Chirality : 0.041 0.172 3227 Planarity : 0.004 0.049 3377 Dihedral : 7.923 153.138 2845 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.79 % Favored : 98.17 % Rotamer: Outliers : 2.53 % Allowed : 15.30 % Favored : 82.17 % 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: 1.76 (0.17), residues: 2516 helix: 1.84 (0.12), residues: 1704 sheet: 1.74 (0.45), residues: 159 loop : -0.76 (0.24), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 68 TYR 0.016 0.001 TYR F 690 PHE 0.047 0.001 PHE D 280 TRP 0.016 0.001 TRP F 833 HIS 0.003 0.001 HIS D 122 Details of bonding type rmsd covalent geometry : bond 0.00272 (19776) covalent geometry : angle 0.55761 (26893) hydrogen bonds : bond 0.04207 ( 1389) hydrogen bonds : angle 4.11462 ( 4119) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 289 time to evaluate : 0.771 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: symmetry clash revert: symmetry clash REVERT: B 7 ARG cc_start: 0.8239 (mtt180) cc_final: 0.7853 (mmm160) REVERT: B 27 ARG cc_start: 0.7651 (ttm-80) cc_final: 0.6583 (ttt180) REVERT: C 7 ARG cc_start: 0.8124 (tmm160) cc_final: 0.7283 (mtt180) REVERT: C 13 LEU cc_start: 0.8595 (OUTLIER) cc_final: 0.8237 (tt) REVERT: D 113 ILE cc_start: 0.8583 (OUTLIER) cc_final: 0.8246 (tp) REVERT: D 195 ASP cc_start: 0.8090 (m-30) cc_final: 0.7682 (m-30) REVERT: D 351 LEU cc_start: 0.8409 (OUTLIER) cc_final: 0.8134 (mm) REVERT: D 417 ASP cc_start: 0.8749 (p0) cc_final: 0.8259 (p0) REVERT: D 815 SER cc_start: 0.8533 (t) cc_final: 0.8104 (m) REVERT: E 153 LEU cc_start: 0.8386 (OUTLIER) cc_final: 0.8069 (mt) REVERT: E 233 LEU cc_start: 0.8759 (mt) cc_final: 0.8550 (mt) REVERT: F 287 GLU cc_start: 0.8523 (OUTLIER) cc_final: 0.8319 (mt-10) REVERT: G 17 GLU cc_start: 0.8160 (tp30) cc_final: 0.7872 (tp30) outliers start: 51 outliers final: 30 residues processed: 319 average time/residue: 0.1229 time to fit residues: 64.1814 Evaluate side-chains 306 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 271 time to evaluate : 0.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain D residue 113 ILE Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 227 ILE Chi-restraints excluded: chain D residue 260 THR Chi-restraints excluded: chain D residue 351 LEU Chi-restraints excluded: chain D residue 738 ILE Chi-restraints excluded: chain D residue 785 CYS Chi-restraints excluded: chain D residue 858 LEU Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 164 GLU Chi-restraints excluded: chain E residue 201 ASP Chi-restraints excluded: chain E residue 387 VAL Chi-restraints excluded: chain E residue 744 GLU Chi-restraints excluded: chain E residue 777 MET Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 92 MET Chi-restraints excluded: chain F residue 124 GLN Chi-restraints excluded: chain F residue 142 SER Chi-restraints excluded: chain F residue 174 GLU Chi-restraints excluded: chain F residue 243 THR Chi-restraints excluded: chain F residue 287 GLU Chi-restraints excluded: chain F residue 353 LEU Chi-restraints excluded: chain F residue 764 MET Chi-restraints excluded: chain F residue 833 TRP Chi-restraints excluded: chain F residue 902 VAL Chi-restraints excluded: chain F residue 914 LEU Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain I residue 28 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 95 optimal weight: 8.9990 chunk 26 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 177 optimal weight: 2.9990 chunk 236 optimal weight: 0.9980 chunk 106 optimal weight: 0.9990 chunk 7 optimal weight: 4.9990 chunk 78 optimal weight: 0.8980 chunk 52 optimal weight: 6.9990 chunk 148 optimal weight: 1.9990 chunk 211 optimal weight: 0.8980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 851 ASN E 440 GLN ** F 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.101390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.085771 restraints weight = 48442.083| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 2.76 r_work: 0.3335 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.2141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 19776 Z= 0.130 Angle : 0.567 9.871 26893 Z= 0.287 Chirality : 0.042 0.182 3227 Planarity : 0.004 0.049 3377 Dihedral : 7.834 153.243 2845 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.99 % Favored : 97.97 % Rotamer: Outliers : 2.72 % Allowed : 16.30 % Favored : 80.98 % 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: 1.87 (0.17), residues: 2516 helix: 1.92 (0.12), residues: 1704 sheet: 1.71 (0.44), residues: 159 loop : -0.70 (0.24), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 68 TYR 0.015 0.001 TYR F 690 PHE 0.042 0.001 PHE D 280 TRP 0.017 0.001 TRP F 833 HIS 0.003 0.001 HIS F 832 Details of bonding type rmsd covalent geometry : bond 0.00291 (19776) covalent geometry : angle 0.56725 (26893) hydrogen bonds : bond 0.04203 ( 1389) hydrogen bonds : angle 4.07745 ( 4119) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 292 time to evaluate : 0.762 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: B 7 ARG cc_start: 0.8226 (mtt180) cc_final: 0.7855 (mmm160) REVERT: B 27 ARG cc_start: 0.7663 (ttm-80) cc_final: 0.6554 (ttt180) REVERT: C 7 ARG cc_start: 0.8126 (tmm160) cc_final: 0.7327 (mtt180) REVERT: D 113 ILE cc_start: 0.8548 (OUTLIER) cc_final: 0.8192 (tp) REVERT: D 195 ASP cc_start: 0.8076 (m-30) cc_final: 0.7696 (m-30) REVERT: D 351 LEU cc_start: 0.8410 (OUTLIER) cc_final: 0.8109 (mm) REVERT: D 417 ASP cc_start: 0.8766 (p0) cc_final: 0.8274 (p0) REVERT: D 815 SER cc_start: 0.8552 (t) cc_final: 0.8123 (m) REVERT: D 858 LEU cc_start: 0.8367 (OUTLIER) cc_final: 0.8104 (tt) REVERT: E 153 LEU cc_start: 0.8396 (OUTLIER) cc_final: 0.8115 (mt) REVERT: E 233 LEU cc_start: 0.8746 (mt) cc_final: 0.8530 (mt) REVERT: E 833 TRP cc_start: 0.8082 (OUTLIER) cc_final: 0.7839 (p-90) REVERT: F 124 GLN cc_start: 0.8675 (OUTLIER) cc_final: 0.8241 (mp10) REVERT: G 17 GLU cc_start: 0.8183 (tp30) cc_final: 0.7928 (tp30) REVERT: G 52 GLU cc_start: 0.8180 (tm-30) cc_final: 0.7721 (tm-30) REVERT: G 79 LYS cc_start: 0.8984 (mptt) cc_final: 0.8750 (mmtt) REVERT: I 17 GLU cc_start: 0.8209 (tp30) cc_final: 0.7645 (tp30) outliers start: 55 outliers final: 33 residues processed: 324 average time/residue: 0.1236 time to fit residues: 65.7590 Evaluate side-chains 305 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 266 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 113 ILE Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 227 ILE Chi-restraints excluded: chain D residue 260 THR Chi-restraints excluded: chain D residue 351 LEU Chi-restraints excluded: chain D residue 785 CYS Chi-restraints excluded: chain D residue 858 LEU Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 164 GLU Chi-restraints excluded: chain E residue 201 ASP Chi-restraints excluded: chain E residue 387 VAL Chi-restraints excluded: chain E residue 744 GLU Chi-restraints excluded: chain E residue 777 MET Chi-restraints excluded: chain E residue 833 TRP Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 92 MET Chi-restraints excluded: chain F residue 124 GLN Chi-restraints excluded: chain F residue 142 SER Chi-restraints excluded: chain F residue 174 GLU Chi-restraints excluded: chain F residue 243 THR Chi-restraints excluded: chain F residue 260 THR Chi-restraints excluded: chain F residue 353 LEU Chi-restraints excluded: chain F residue 764 MET Chi-restraints excluded: chain F residue 833 TRP Chi-restraints excluded: chain F residue 902 VAL Chi-restraints excluded: chain F residue 914 LEU Chi-restraints excluded: chain G residue 26 GLU Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain I residue 77 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 128 optimal weight: 6.9990 chunk 8 optimal weight: 0.9990 chunk 31 optimal weight: 3.9990 chunk 200 optimal weight: 0.7980 chunk 188 optimal weight: 3.9990 chunk 248 optimal weight: 3.9990 chunk 100 optimal weight: 1.9990 chunk 233 optimal weight: 2.9990 chunk 238 optimal weight: 1.9990 chunk 67 optimal weight: 0.4980 chunk 158 optimal weight: 1.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 440 GLN ** F 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.100706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.085006 restraints weight = 48839.867| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 2.77 r_work: 0.3319 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.2254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 19776 Z= 0.147 Angle : 0.592 10.626 26893 Z= 0.302 Chirality : 0.043 0.245 3227 Planarity : 0.004 0.051 3377 Dihedral : 7.851 154.244 2845 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.07 % Favored : 97.89 % Rotamer: Outliers : 2.87 % Allowed : 16.99 % Favored : 80.14 % 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: 1.86 (0.17), residues: 2516 helix: 1.90 (0.12), residues: 1707 sheet: 1.59 (0.45), residues: 162 loop : -0.66 (0.24), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 68 TYR 0.014 0.001 TYR F 690 PHE 0.068 0.001 PHE D 280 TRP 0.017 0.001 TRP F 833 HIS 0.003 0.001 HIS F 832 Details of bonding type rmsd covalent geometry : bond 0.00341 (19776) covalent geometry : angle 0.59250 (26893) hydrogen bonds : bond 0.04346 ( 1389) hydrogen bonds : angle 4.13695 ( 4119) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 283 time to evaluate : 0.586 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: B 7 ARG cc_start: 0.8286 (mtt180) cc_final: 0.7878 (mmm160) REVERT: B 27 ARG cc_start: 0.7664 (ttm-80) cc_final: 0.6548 (ttt180) REVERT: C 7 ARG cc_start: 0.8178 (tmm160) cc_final: 0.7320 (mtt180) REVERT: D 113 ILE cc_start: 0.8523 (OUTLIER) cc_final: 0.8153 (tp) REVERT: D 195 ASP cc_start: 0.8078 (m-30) cc_final: 0.7724 (m-30) REVERT: D 351 LEU cc_start: 0.8391 (OUTLIER) cc_final: 0.8096 (mm) REVERT: D 417 ASP cc_start: 0.8752 (p0) cc_final: 0.8256 (p0) REVERT: D 815 SER cc_start: 0.8640 (t) cc_final: 0.8208 (m) REVERT: D 858 LEU cc_start: 0.8423 (OUTLIER) cc_final: 0.8200 (tt) REVERT: E 153 LEU cc_start: 0.8399 (OUTLIER) cc_final: 0.8123 (mt) REVERT: E 233 LEU cc_start: 0.8734 (mt) cc_final: 0.8531 (mt) REVERT: E 302 MET cc_start: 0.7881 (ppp) cc_final: 0.7632 (ppp) REVERT: E 343 MET cc_start: 0.8862 (mmm) cc_final: 0.8556 (mmm) REVERT: E 833 TRP cc_start: 0.8146 (OUTLIER) cc_final: 0.7921 (p-90) REVERT: F 124 GLN cc_start: 0.8672 (OUTLIER) cc_final: 0.8237 (mp10) REVERT: G 17 GLU cc_start: 0.8204 (tp30) cc_final: 0.7933 (tp30) REVERT: G 52 GLU cc_start: 0.8269 (tm-30) cc_final: 0.7661 (tm-30) REVERT: G 79 LYS cc_start: 0.9001 (mptt) cc_final: 0.8782 (mmtt) outliers start: 58 outliers final: 37 residues processed: 316 average time/residue: 0.1154 time to fit residues: 59.7173 Evaluate side-chains 315 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 272 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 113 ILE Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 227 ILE Chi-restraints excluded: chain D residue 260 THR Chi-restraints excluded: chain D residue 351 LEU Chi-restraints excluded: chain D residue 738 ILE Chi-restraints excluded: chain D residue 776 LEU Chi-restraints excluded: chain D residue 785 CYS Chi-restraints excluded: chain D residue 858 LEU Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 164 GLU Chi-restraints excluded: chain E residue 201 ASP Chi-restraints excluded: chain E residue 234 THR Chi-restraints excluded: chain E residue 387 VAL Chi-restraints excluded: chain E residue 690 TYR Chi-restraints excluded: chain E residue 744 GLU Chi-restraints excluded: chain E residue 777 MET Chi-restraints excluded: chain E residue 833 TRP Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 92 MET Chi-restraints excluded: chain F residue 124 GLN Chi-restraints excluded: chain F residue 142 SER Chi-restraints excluded: chain F residue 174 GLU Chi-restraints excluded: chain F residue 243 THR Chi-restraints excluded: chain F residue 260 THR Chi-restraints excluded: chain F residue 353 LEU Chi-restraints excluded: chain F residue 764 MET Chi-restraints excluded: chain F residue 833 TRP Chi-restraints excluded: chain F residue 894 SER Chi-restraints excluded: chain F residue 902 VAL Chi-restraints excluded: chain F residue 914 LEU Chi-restraints excluded: chain G residue 26 GLU Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain I residue 77 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 222 optimal weight: 0.7980 chunk 195 optimal weight: 0.0770 chunk 13 optimal weight: 1.9990 chunk 171 optimal weight: 1.9990 chunk 88 optimal weight: 4.9990 chunk 91 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 96 optimal weight: 8.9990 chunk 148 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 12 optimal weight: 0.3980 overall best weight: 1.0542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 440 GLN ** F 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.101078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.085379 restraints weight = 48675.766| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 2.77 r_work: 0.3323 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.2348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 19776 Z= 0.139 Angle : 0.618 12.301 26893 Z= 0.308 Chirality : 0.043 0.222 3227 Planarity : 0.004 0.052 3377 Dihedral : 7.803 153.770 2845 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.07 % Favored : 97.89 % Rotamer: Outliers : 2.82 % Allowed : 17.43 % Favored : 79.74 % 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: 1.87 (0.17), residues: 2516 helix: 1.90 (0.12), residues: 1707 sheet: 1.73 (0.45), residues: 159 loop : -0.65 (0.24), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 68 TYR 0.014 0.001 TYR F 690 PHE 0.069 0.001 PHE D 280 TRP 0.018 0.001 TRP F 833 HIS 0.003 0.001 HIS F 832 Details of bonding type rmsd covalent geometry : bond 0.00319 (19776) covalent geometry : angle 0.61771 (26893) hydrogen bonds : bond 0.04269 ( 1389) hydrogen bonds : angle 4.14072 ( 4119) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 285 time to evaluate : 0.596 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: B 7 ARG cc_start: 0.8271 (mtt180) cc_final: 0.7868 (mmm160) REVERT: B 27 ARG cc_start: 0.7695 (ttm-80) cc_final: 0.6540 (ttt180) REVERT: C 7 ARG cc_start: 0.8143 (tmm160) cc_final: 0.7308 (mtt180) REVERT: D 113 ILE cc_start: 0.8544 (OUTLIER) cc_final: 0.8153 (tp) REVERT: D 195 ASP cc_start: 0.8064 (m-30) cc_final: 0.7755 (m-30) REVERT: D 343 MET cc_start: 0.8651 (tpt) cc_final: 0.8286 (mmm) REVERT: D 351 LEU cc_start: 0.8360 (OUTLIER) cc_final: 0.8064 (mm) REVERT: D 417 ASP cc_start: 0.8759 (p0) cc_final: 0.8259 (p0) REVERT: D 815 SER cc_start: 0.8621 (t) cc_final: 0.8194 (m) REVERT: D 858 LEU cc_start: 0.8474 (OUTLIER) cc_final: 0.8255 (tt) REVERT: D 888 PHE cc_start: 0.8468 (t80) cc_final: 0.8246 (t80) REVERT: E 153 LEU cc_start: 0.8393 (OUTLIER) cc_final: 0.8148 (mt) REVERT: E 302 MET cc_start: 0.7867 (ppp) cc_final: 0.7604 (ppp) REVERT: E 343 MET cc_start: 0.8864 (mmm) cc_final: 0.8626 (mmm) REVERT: E 833 TRP cc_start: 0.8127 (OUTLIER) cc_final: 0.7842 (p-90) REVERT: F 27 MET cc_start: 0.8246 (mmp) cc_final: 0.7932 (mmp) REVERT: F 124 GLN cc_start: 0.8683 (OUTLIER) cc_final: 0.8250 (mp10) REVERT: G 17 GLU cc_start: 0.8217 (tp30) cc_final: 0.7965 (tp30) REVERT: G 79 LYS cc_start: 0.9027 (mptt) cc_final: 0.8798 (mmtt) REVERT: I 17 GLU cc_start: 0.8232 (tp30) cc_final: 0.7671 (tp30) outliers start: 57 outliers final: 38 residues processed: 319 average time/residue: 0.1036 time to fit residues: 54.3257 Evaluate side-chains 311 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 267 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ILE Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain D residue 92 MET Chi-restraints excluded: chain D residue 113 ILE Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 227 ILE Chi-restraints excluded: chain D residue 260 THR Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 351 LEU Chi-restraints excluded: chain D residue 738 ILE Chi-restraints excluded: chain D residue 776 LEU Chi-restraints excluded: chain D residue 785 CYS Chi-restraints excluded: chain D residue 858 LEU Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 164 GLU Chi-restraints excluded: chain E residue 201 ASP Chi-restraints excluded: chain E residue 218 MET Chi-restraints excluded: chain E residue 387 VAL Chi-restraints excluded: chain E residue 690 TYR Chi-restraints excluded: chain E residue 744 GLU Chi-restraints excluded: chain E residue 777 MET Chi-restraints excluded: chain E residue 833 TRP Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 92 MET Chi-restraints excluded: chain F residue 124 GLN Chi-restraints excluded: chain F residue 142 SER Chi-restraints excluded: chain F residue 174 GLU Chi-restraints excluded: chain F residue 243 THR Chi-restraints excluded: chain F residue 260 THR Chi-restraints excluded: chain F residue 353 LEU Chi-restraints excluded: chain F residue 764 MET Chi-restraints excluded: chain F residue 833 TRP Chi-restraints excluded: chain F residue 902 VAL Chi-restraints excluded: chain F residue 914 LEU Chi-restraints excluded: chain G residue 26 GLU Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain I residue 77 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 57 optimal weight: 0.7980 chunk 125 optimal weight: 3.9990 chunk 144 optimal weight: 0.6980 chunk 85 optimal weight: 6.9990 chunk 95 optimal weight: 7.9990 chunk 40 optimal weight: 0.8980 chunk 200 optimal weight: 0.7980 chunk 218 optimal weight: 2.9990 chunk 82 optimal weight: 0.9980 chunk 133 optimal weight: 0.7980 chunk 43 optimal weight: 6.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 440 GLN ** F 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.101607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.086256 restraints weight = 48387.517| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 2.74 r_work: 0.3343 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.2428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 19776 Z= 0.128 Angle : 0.608 11.420 26893 Z= 0.304 Chirality : 0.043 0.238 3227 Planarity : 0.004 0.053 3377 Dihedral : 7.691 152.677 2845 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.95 % Favored : 98.01 % Rotamer: Outliers : 2.08 % Allowed : 18.67 % Favored : 79.25 % 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: 1.89 (0.17), residues: 2516 helix: 1.91 (0.12), residues: 1707 sheet: 1.61 (0.45), residues: 162 loop : -0.59 (0.24), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 68 TYR 0.014 0.001 TYR F 690 PHE 0.065 0.001 PHE D 280 TRP 0.018 0.001 TRP F 833 HIS 0.003 0.001 HIS F 832 Details of bonding type rmsd covalent geometry : bond 0.00289 (19776) covalent geometry : angle 0.60794 (26893) hydrogen bonds : bond 0.04137 ( 1389) hydrogen bonds : angle 4.15164 ( 4119) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 285 time to evaluate : 0.717 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: B 7 ARG cc_start: 0.8300 (mtt180) cc_final: 0.7905 (mmm160) REVERT: B 27 ARG cc_start: 0.7669 (ttm-80) cc_final: 0.6520 (ttt180) REVERT: C 7 ARG cc_start: 0.8181 (tmm160) cc_final: 0.7324 (mtt180) REVERT: D 27 MET cc_start: 0.7785 (tpp) cc_final: 0.7268 (tmm) REVERT: D 113 ILE cc_start: 0.8471 (OUTLIER) cc_final: 0.8038 (tp) REVERT: D 195 ASP cc_start: 0.8039 (m-30) cc_final: 0.7765 (m-30) REVERT: D 343 MET cc_start: 0.8621 (tpt) cc_final: 0.8268 (mmm) REVERT: D 351 LEU cc_start: 0.8340 (OUTLIER) cc_final: 0.8049 (mm) REVERT: D 417 ASP cc_start: 0.8755 (p0) cc_final: 0.8248 (p0) REVERT: D 815 SER cc_start: 0.8598 (t) cc_final: 0.8178 (m) REVERT: D 858 LEU cc_start: 0.8425 (OUTLIER) cc_final: 0.8223 (tt) REVERT: E 153 LEU cc_start: 0.8285 (OUTLIER) cc_final: 0.8066 (mt) REVERT: E 302 MET cc_start: 0.7863 (ppp) cc_final: 0.7589 (ppp) REVERT: E 343 MET cc_start: 0.8868 (mmm) cc_final: 0.8658 (mmm) REVERT: E 833 TRP cc_start: 0.8062 (OUTLIER) cc_final: 0.7837 (p-90) REVERT: F 27 MET cc_start: 0.8168 (mmp) cc_final: 0.7873 (mmp) REVERT: F 124 GLN cc_start: 0.8681 (OUTLIER) cc_final: 0.8252 (mp10) REVERT: F 235 MET cc_start: 0.7744 (mtt) cc_final: 0.7537 (mtt) REVERT: G 17 GLU cc_start: 0.8145 (tp30) cc_final: 0.7882 (tp30) REVERT: G 79 LYS cc_start: 0.9032 (mptt) cc_final: 0.8799 (mmtt) REVERT: H 17 GLU cc_start: 0.7468 (tp30) cc_final: 0.7265 (tp30) REVERT: I 14 GLU cc_start: 0.8490 (tp30) cc_final: 0.8040 (tp30) REVERT: I 31 LYS cc_start: 0.7845 (ptpp) cc_final: 0.7357 (ptpp) outliers start: 42 outliers final: 31 residues processed: 308 average time/residue: 0.1067 time to fit residues: 53.5807 Evaluate side-chains 309 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 272 time to evaluate : 0.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 113 ILE Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 260 THR Chi-restraints excluded: chain D residue 351 LEU Chi-restraints excluded: chain D residue 776 LEU Chi-restraints excluded: chain D residue 785 CYS Chi-restraints excluded: chain D residue 858 LEU Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 164 GLU Chi-restraints excluded: chain E residue 201 ASP Chi-restraints excluded: chain E residue 387 VAL Chi-restraints excluded: chain E residue 690 TYR Chi-restraints excluded: chain E residue 744 GLU Chi-restraints excluded: chain E residue 777 MET Chi-restraints excluded: chain E residue 833 TRP Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 92 MET Chi-restraints excluded: chain F residue 124 GLN Chi-restraints excluded: chain F residue 142 SER Chi-restraints excluded: chain F residue 174 GLU Chi-restraints excluded: chain F residue 243 THR Chi-restraints excluded: chain F residue 260 THR Chi-restraints excluded: chain F residue 353 LEU Chi-restraints excluded: chain F residue 764 MET Chi-restraints excluded: chain F residue 833 TRP Chi-restraints excluded: chain F residue 902 VAL Chi-restraints excluded: chain F residue 914 LEU Chi-restraints excluded: chain G residue 26 GLU Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain I residue 28 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 172 optimal weight: 0.8980 chunk 115 optimal weight: 0.6980 chunk 6 optimal weight: 10.0000 chunk 133 optimal weight: 0.9990 chunk 212 optimal weight: 4.9990 chunk 102 optimal weight: 3.9990 chunk 168 optimal weight: 1.9990 chunk 124 optimal weight: 0.8980 chunk 12 optimal weight: 0.2980 chunk 3 optimal weight: 7.9990 chunk 147 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 440 GLN ** F 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.102070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.086446 restraints weight = 48652.141| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 2.77 r_work: 0.3344 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.2510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 19776 Z= 0.129 Angle : 0.627 13.155 26893 Z= 0.310 Chirality : 0.043 0.259 3227 Planarity : 0.004 0.052 3377 Dihedral : 7.607 152.579 2845 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.11 % Favored : 97.85 % Rotamer: Outliers : 2.03 % Allowed : 19.22 % Favored : 78.75 % 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: 1.91 (0.17), residues: 2516 helix: 1.94 (0.12), residues: 1689 sheet: 1.75 (0.45), residues: 159 loop : -0.60 (0.24), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 68 TYR 0.014 0.001 TYR F 690 PHE 0.062 0.001 PHE D 280 TRP 0.018 0.001 TRP F 833 HIS 0.002 0.001 HIS F 832 Details of bonding type rmsd covalent geometry : bond 0.00292 (19776) covalent geometry : angle 0.62653 (26893) hydrogen bonds : bond 0.04099 ( 1389) hydrogen bonds : angle 4.15880 ( 4119) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 282 time to evaluate : 0.597 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: B 7 ARG cc_start: 0.8314 (mtt180) cc_final: 0.7905 (mmm160) REVERT: B 27 ARG cc_start: 0.7641 (ttm-80) cc_final: 0.6479 (ttt180) REVERT: C 7 ARG cc_start: 0.8190 (tmm160) cc_final: 0.7329 (mtt180) REVERT: D 27 MET cc_start: 0.7756 (tpp) cc_final: 0.7254 (tmm) REVERT: D 113 ILE cc_start: 0.8465 (OUTLIER) cc_final: 0.8023 (tp) REVERT: D 195 ASP cc_start: 0.7984 (m-30) cc_final: 0.7767 (m-30) REVERT: D 343 MET cc_start: 0.8627 (tpt) cc_final: 0.8268 (mmm) REVERT: D 351 LEU cc_start: 0.8347 (OUTLIER) cc_final: 0.8061 (mm) REVERT: D 417 ASP cc_start: 0.8775 (p0) cc_final: 0.8253 (p0) REVERT: D 815 SER cc_start: 0.8588 (t) cc_final: 0.8173 (m) REVERT: D 888 PHE cc_start: 0.8410 (t80) cc_final: 0.8202 (t80) REVERT: E 153 LEU cc_start: 0.8277 (OUTLIER) cc_final: 0.8055 (mt) REVERT: E 302 MET cc_start: 0.7785 (ppp) cc_final: 0.7515 (ppp) REVERT: E 343 MET cc_start: 0.8849 (mmm) cc_final: 0.8637 (mmm) REVERT: F 27 MET cc_start: 0.8167 (mmp) cc_final: 0.7892 (mmp) REVERT: F 124 GLN cc_start: 0.8691 (OUTLIER) cc_final: 0.8263 (mp10) REVERT: G 17 GLU cc_start: 0.8204 (tp30) cc_final: 0.7946 (tp30) REVERT: G 52 GLU cc_start: 0.8423 (tm-30) cc_final: 0.8199 (tm-30) REVERT: G 79 LYS cc_start: 0.9044 (mptt) cc_final: 0.8806 (mmtt) outliers start: 41 outliers final: 31 residues processed: 306 average time/residue: 0.1121 time to fit residues: 56.2280 Evaluate side-chains 312 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 277 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain D residue 64 MET Chi-restraints excluded: chain D residue 113 ILE Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 227 ILE Chi-restraints excluded: chain D residue 260 THR Chi-restraints excluded: chain D residue 351 LEU Chi-restraints excluded: chain D residue 776 LEU Chi-restraints excluded: chain D residue 785 CYS Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 201 ASP Chi-restraints excluded: chain E residue 387 VAL Chi-restraints excluded: chain E residue 690 TYR Chi-restraints excluded: chain E residue 744 GLU Chi-restraints excluded: chain E residue 777 MET Chi-restraints excluded: chain F residue 92 MET Chi-restraints excluded: chain F residue 124 GLN Chi-restraints excluded: chain F residue 142 SER Chi-restraints excluded: chain F residue 174 GLU Chi-restraints excluded: chain F residue 243 THR Chi-restraints excluded: chain F residue 260 THR Chi-restraints excluded: chain F residue 353 LEU Chi-restraints excluded: chain F residue 764 MET Chi-restraints excluded: chain F residue 833 TRP Chi-restraints excluded: chain F residue 902 VAL Chi-restraints excluded: chain F residue 914 LEU Chi-restraints excluded: chain G residue 26 GLU Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain I residue 28 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 165 optimal weight: 3.9990 chunk 204 optimal weight: 5.9990 chunk 33 optimal weight: 0.7980 chunk 248 optimal weight: 1.9990 chunk 152 optimal weight: 2.9990 chunk 161 optimal weight: 4.9990 chunk 192 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 113 optimal weight: 0.0060 chunk 211 optimal weight: 0.9980 chunk 179 optimal weight: 0.9980 overall best weight: 0.7598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 440 GLN ** F 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.102074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.086523 restraints weight = 48482.116| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 2.77 r_work: 0.3347 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.2581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 19776 Z= 0.128 Angle : 0.624 14.922 26893 Z= 0.310 Chirality : 0.043 0.260 3227 Planarity : 0.004 0.053 3377 Dihedral : 7.547 152.664 2845 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.95 % Favored : 98.01 % Rotamer: Outliers : 1.98 % Allowed : 19.86 % Favored : 78.16 % 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: 1.91 (0.17), residues: 2516 helix: 1.94 (0.12), residues: 1689 sheet: 1.74 (0.45), residues: 159 loop : -0.60 (0.24), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 68 TYR 0.014 0.001 TYR F 690 PHE 0.074 0.001 PHE D 280 TRP 0.028 0.001 TRP E 833 HIS 0.002 0.001 HIS F 832 Details of bonding type rmsd covalent geometry : bond 0.00289 (19776) covalent geometry : angle 0.62414 (26893) hydrogen bonds : bond 0.04061 ( 1389) hydrogen bonds : angle 4.16259 ( 4119) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3773.65 seconds wall clock time: 65 minutes 43.80 seconds (3943.80 seconds total)