Starting phenix.real_space_refine on Thu Feb 5 19:49:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9rfu_53941/02_2026/9rfu_53941.cif Found real_map, /net/cci-nas-00/data/ceres_data/9rfu_53941/02_2026/9rfu_53941.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9rfu_53941/02_2026/9rfu_53941.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9rfu_53941/02_2026/9rfu_53941.map" model { file = "/net/cci-nas-00/data/ceres_data/9rfu_53941/02_2026/9rfu_53941.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9rfu_53941/02_2026/9rfu_53941.cif" } resolution = 3.3 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 64 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: "F" 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: 5.04, per 1000 atoms: 0.26 Number of scatterers: 19410 At special positions: 0 Unit cell: (118.42, 125.105, 140.385, 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: 2.94 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 113 helices and 8 sheets defined 72.5% alpha, 5.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.52 Creating SS restraints... Processing helix chain 'A' and resid 1 through 7 removed outlier: 4.016A pdb=" N LEU A 5 " --> pdb=" O SER A 1 " (cutoff:3.500A) Processing helix chain 'A' and resid 8 through 30 removed outlier: 3.551A pdb=" N LEU A 12 " --> pdb=" O ALA A 8 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N THR A 30 " --> pdb=" O GLN A 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 7 Processing helix chain 'B' and resid 8 through 30 removed outlier: 3.531A pdb=" N LEU B 12 " --> pdb=" O ALA B 8 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 8 Processing helix chain 'C' and resid 8 through 30 removed outlier: 3.851A pdb=" N LEU C 12 " --> pdb=" O ALA C 8 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N THR C 30 " --> pdb=" O GLN C 26 " (cutoff:3.500A) Processing helix chain 'D' and resid 22 through 31 removed outlier: 3.562A pdb=" N ARG D 26 " --> pdb=" O PRO D 22 " (cutoff:3.500A) Processing helix chain 'D' and resid 31 through 49 Processing helix chain 'D' and resid 52 through 60 removed outlier: 3.670A pdb=" N GLN D 60 " --> pdb=" O VAL D 56 " (cutoff:3.500A) Processing helix chain 'D' and resid 69 through 83 Processing helix chain 'D' and resid 102 through 119 removed outlier: 3.602A pdb=" N ASP D 119 " --> pdb=" O ARG D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 135 through 140 removed outlier: 3.672A pdb=" N GLN D 140 " --> pdb=" O THR D 137 " (cutoff:3.500A) Processing helix chain 'D' and resid 159 through 175 removed outlier: 3.585A pdb=" N ASN D 163 " --> pdb=" O GLU D 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 189 through 224 removed outlier: 4.436A pdb=" N GLN D 205 " --> pdb=" O ASP D 201 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N VAL D 206 " --> pdb=" O ARG D 202 " (cutoff:3.500A) Processing helix chain 'D' and resid 226 through 253 removed outlier: 3.839A pdb=" N HIS D 253 " --> pdb=" O PHE D 249 " (cutoff:3.500A) Processing helix chain 'D' and resid 259 through 292 removed outlier: 3.593A pdb=" N GLY D 292 " --> pdb=" O ALA D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 294 through 324 removed outlier: 5.905A pdb=" N HIS D 308 " --> pdb=" O GLY D 304 " (cutoff:3.500A) removed outlier: 5.430A 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 336 through 365 removed outlier: 3.538A pdb=" N ALA D 340 " --> pdb=" O GLY D 336 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N GLY D 354 " --> pdb=" O ALA D 350 " (cutoff:3.500A) Proline residue: D 355 - end of helix removed outlier: 3.740A pdb=" N GLY D 365 " --> pdb=" O THR D 361 " (cutoff:3.500A) Processing helix chain 'D' and resid 374 through 389 removed outlier: 3.652A pdb=" N GLY D 378 " --> pdb=" O ALA D 374 " (cutoff:3.500A) Processing helix chain 'D' and resid 389 through 406 removed outlier: 3.989A pdb=" N ILE D 393 " --> pdb=" O TRP D 389 " (cutoff:3.500A) Processing helix chain 'D' and resid 417 through 421 removed outlier: 3.548A pdb=" N TYR D 420 " --> pdb=" O ASP D 417 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU D 421 " --> pdb=" O ARG D 418 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 417 through 421' 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: 3.519A pdb=" N PHE D 696 " --> pdb=" O PRO D 693 " (cutoff:3.500A) Processing helix chain 'D' and resid 698 through 709 Processing helix chain 'D' and resid 728 through 746 removed outlier: 4.503A pdb=" N ILE D 735 " --> pdb=" O GLY D 731 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N ALA D 736 " --> pdb=" O ILE D 732 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N LYS D 737 " --> pdb=" O ALA D 733 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ILE D 746 " --> pdb=" O ALA D 742 " (cutoff:3.500A) Processing helix chain 'D' and resid 761 through 796 Processing helix chain 'D' and resid 797 through 824 removed outlier: 3.847A pdb=" N ALA D 801 " --> pdb=" O SER D 797 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA D 802 " --> pdb=" O VAL D 798 " (cutoff:3.500A) Processing helix chain 'D' and resid 834 through 861 Processing helix chain 'D' and resid 865 through 894 removed outlier: 4.718A pdb=" N SER D 879 " --> pdb=" O GLY D 875 " (cutoff:3.500A) removed outlier: 4.787A 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 920 through 925 Processing helix chain 'D' and resid 925 through 934 Processing helix chain 'D' and resid 935 through 938 removed outlier: 3.524A pdb=" N TRP D 938 " --> pdb=" O LYS D 935 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 935 through 938' Processing helix chain 'E' and resid 22 through 31 removed outlier: 3.531A pdb=" N ARG E 26 " --> pdb=" O PRO E 22 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N PHE E 31 " --> pdb=" O MET E 27 " (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 83 Processing helix chain 'E' and resid 102 through 119 removed outlier: 3.781A pdb=" N ASP E 119 " --> pdb=" O ARG E 115 " (cutoff:3.500A) Processing helix chain 'E' and resid 135 through 140 Processing helix chain 'E' and resid 159 through 176 removed outlier: 3.713A pdb=" N ASN E 163 " --> pdb=" O GLU E 159 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N LEU E 176 " --> pdb=" O ILE E 172 " (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: 3.814A pdb=" N HIS E 253 " --> pdb=" O PHE E 249 " (cutoff:3.500A) Processing helix chain 'E' and resid 259 through 292 removed outlier: 3.588A pdb=" N GLY E 292 " --> pdb=" O ALA E 288 " (cutoff:3.500A) Processing helix chain 'E' and resid 296 through 324 removed outlier: 5.541A pdb=" N HIS E 308 " --> pdb=" O GLY E 304 " (cutoff:3.500A) removed outlier: 5.268A pdb=" N VAL E 309 " --> pdb=" O GLY E 305 " (cutoff:3.500A) Processing helix chain 'E' and resid 325 through 327 No H-bonds generated for 'chain 'E' and resid 325 through 327' Processing helix chain 'E' and resid 329 through 334 Processing helix chain 'E' and resid 335 through 365 removed outlier: 3.742A pdb=" N LEU E 339 " --> pdb=" O LEU E 335 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLY E 354 " --> pdb=" O ALA E 350 " (cutoff:3.500A) Proline residue: E 355 - end of helix removed outlier: 3.770A pdb=" N GLY E 365 " --> pdb=" O THR E 361 " (cutoff:3.500A) Processing helix chain 'E' and resid 374 through 389 removed outlier: 4.065A pdb=" N GLY E 378 " --> pdb=" O ALA E 374 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N TRP E 389 " --> pdb=" O ALA E 385 " (cutoff:3.500A) Processing helix chain 'E' and resid 389 through 406 removed outlier: 3.684A pdb=" N ILE E 393 " --> pdb=" O TRP E 389 " (cutoff:3.500A) Processing helix chain 'E' and resid 417 through 421 Processing helix chain 'E' and resid 425 through 438 removed outlier: 4.375A 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 694 through 697 removed outlier: 3.610A pdb=" N ASP E 697 " --> pdb=" O GLU E 694 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 694 through 697' Processing helix chain 'E' and resid 698 through 709 Processing helix chain 'E' and resid 728 through 746 removed outlier: 4.093A pdb=" N ILE E 735 " --> pdb=" O GLY E 731 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N ALA E 736 " --> pdb=" O ILE E 732 " (cutoff:3.500A) removed outlier: 4.076A 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 824 removed outlier: 3.821A pdb=" N ALA E 801 " --> pdb=" O SER E 797 " (cutoff:3.500A) Processing helix chain 'E' and resid 833 through 861 removed outlier: 3.516A pdb=" N GLU E 861 " --> pdb=" O ARG E 857 " (cutoff:3.500A) Processing helix chain 'E' and resid 866 through 894 removed outlier: 5.232A pdb=" N SER E 879 " --> pdb=" O GLY E 875 " (cutoff:3.500A) removed outlier: 4.849A 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 924 through 934 removed outlier: 3.508A pdb=" N SER E 928 " --> pdb=" O PHE E 924 " (cutoff:3.500A) Processing helix chain 'E' and resid 935 through 938 removed outlier: 3.804A 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 removed outlier: 3.921A pdb=" N ARG F 26 " --> pdb=" O PRO F 22 " (cutoff:3.500A) Processing helix chain 'F' and resid 31 through 50 removed outlier: 3.738A 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: 3.736A pdb=" N ASP F 119 " --> pdb=" O ARG F 115 " (cutoff:3.500A) Processing helix chain 'F' and resid 136 through 140 removed outlier: 3.716A pdb=" N GLN F 140 " --> pdb=" O THR F 137 " (cutoff:3.500A) Processing helix chain 'F' and resid 159 through 175 removed outlier: 3.814A pdb=" N ASN F 163 " --> pdb=" O GLU F 159 " (cutoff:3.500A) Processing helix chain 'F' and resid 188 through 201 removed outlier: 4.074A pdb=" N ASP F 201 " --> pdb=" O GLN F 197 " (cutoff:3.500A) Processing helix chain 'F' and resid 204 through 224 Processing helix chain 'F' and resid 226 through 253 removed outlier: 3.678A pdb=" N HIS F 253 " --> pdb=" O PHE F 249 " (cutoff:3.500A) Processing helix chain 'F' and resid 259 through 292 removed outlier: 3.897A pdb=" N GLY F 292 " --> pdb=" O ALA F 288 " (cutoff:3.500A) Processing helix chain 'F' and resid 294 through 324 removed outlier: 3.823A pdb=" N TYR F 299 " --> pdb=" O ARG F 295 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N TYR F 300 " --> pdb=" O GLU F 296 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N HIS F 308 " --> pdb=" O GLY F 304 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N VAL F 309 " --> pdb=" O GLY F 305 " (cutoff:3.500A) Processing helix chain 'F' and resid 325 through 327 No H-bonds generated for 'chain 'F' and resid 325 through 327' Processing helix chain 'F' and resid 329 through 334 Processing helix chain 'F' and resid 336 through 365 removed outlier: 3.833A pdb=" N GLY F 354 " --> pdb=" O ALA F 350 " (cutoff:3.500A) Proline residue: F 355 - end of helix removed outlier: 3.763A 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: 3.741A pdb=" N ILE F 393 " --> pdb=" O TRP F 389 " (cutoff:3.500A) Processing helix chain 'F' and resid 417 through 421 Processing helix chain 'F' and resid 425 through 438 Processing helix chain 'F' and resid 458 through 474 removed outlier: 3.501A pdb=" N PHE F 462 " --> pdb=" O ASN F 458 " (cutoff:3.500A) Processing helix chain 'F' and resid 692 through 697 removed outlier: 3.877A pdb=" N PHE F 696 " --> pdb=" O PRO F 693 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ASP F 697 " --> pdb=" O GLU F 694 " (cutoff:3.500A) Processing helix chain 'F' and resid 698 through 709 Processing helix chain 'F' and resid 728 through 733 removed outlier: 3.611A pdb=" N ALA F 733 " --> pdb=" O GLN F 729 " (cutoff:3.500A) Processing helix chain 'F' and resid 733 through 747 removed outlier: 4.049A pdb=" N LYS F 737 " --> pdb=" O ALA F 733 " (cutoff:3.500A) Processing helix chain 'F' and resid 761 through 796 removed outlier: 3.502A pdb=" N THR F 795 " --> pdb=" O MET F 791 " (cutoff:3.500A) Processing helix chain 'F' and resid 797 through 825 removed outlier: 3.758A pdb=" N ALA F 801 " --> pdb=" O SER F 797 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ALA F 802 " --> pdb=" O VAL F 798 " (cutoff:3.500A) Processing helix chain 'F' and resid 833 through 862 Processing helix chain 'F' and resid 865 through 894 removed outlier: 4.892A pdb=" N SER F 879 " --> pdb=" O GLY F 875 " (cutoff:3.500A) removed outlier: 5.367A 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 925 Processing helix chain 'F' and resid 925 through 934 Processing helix chain 'F' and resid 935 through 938 removed outlier: 3.565A pdb=" N TRP F 938 " --> pdb=" O LYS F 935 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 935 through 938' Processing helix chain 'G' and resid 5 through 20 Processing helix chain 'G' and resid 23 through 27 Processing helix chain 'G' and resid 33 through 38 Processing helix chain 'G' and resid 41 through 56 Processing helix chain 'G' and resid 69 through 80 Processing helix chain 'H' and resid 4 through 21 Processing helix chain 'H' and resid 42 through 56 removed outlier: 3.905A 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 32 through 37 removed outlier: 3.634A pdb=" N ASP I 36 " --> pdb=" O SER I 32 " (cutoff:3.500A) Processing helix chain 'I' and resid 41 through 55 removed outlier: 3.614A pdb=" N VAL I 45 " --> pdb=" O 4HH I 41 " (cutoff:3.500A) Processing helix chain 'I' and resid 69 through 80 removed outlier: 3.703A pdb=" N LEU I 80 " --> pdb=" O TYR I 76 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 123 through 127 removed outlier: 3.800A pdb=" N SER D 125 " --> pdb=" O LYS D 152 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N GLN D 150 " --> pdb=" O GLN D 127 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N SER D 89 " --> pdb=" O LEU D 153 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLU D 96 " --> pdb=" O LYS D 183 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 123 through 127 removed outlier: 3.800A pdb=" N SER D 125 " --> pdb=" O LYS D 152 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N GLN D 150 " --> pdb=" O GLN D 127 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N SER D 89 " --> pdb=" O LEU D 153 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 480 through 482 removed outlier: 3.611A pdb=" N ARG D 480 " --> pdb=" O SER D 721 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER D 721 " --> pdb=" O ARG D 480 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 125 through 127 removed outlier: 3.980A pdb=" N SER E 125 " --> pdb=" O LYS E 152 " (cutoff:3.500A) removed outlier: 4.055A 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 removed outlier: 3.519A pdb=" N ARG E 480 " --> pdb=" O SER E 721 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 125 through 127 removed outlier: 3.603A pdb=" N SER F 125 " --> pdb=" O LYS F 152 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N GLN F 150 " --> pdb=" O GLN F 127 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL F 94 " --> pdb=" O TYR F 185 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 413 through 414 Processing sheet with id=AA8, first strand: chain 'F' and resid 478 through 482 removed outlier: 3.653A pdb=" N ALA F 755 " --> pdb=" O GLU F 451 " (cutoff:3.500A) 1404 hydrogen bonds defined for protein. 4143 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: 3.87 Time building geometry restraints manager: 3.53 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: 3140 1.31 - 1.43: 4893 1.43 - 1.56: 11563 1.56 - 1.69: 9 1.69 - 1.81: 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 1.489 0.135 2.00e-02 2.50e+03 4.57e+01 bond pdb=" OG 4HH I 41 " pdb=" P 4HH I 41 " ideal model delta sigma weight residual 1.624 1.491 0.133 2.00e-02 2.50e+03 4.41e+01 bond pdb=" OG 4HH G 41 " pdb=" P 4HH G 41 " ideal model delta sigma weight residual 1.624 1.501 0.123 2.00e-02 2.50e+03 3.78e+01 bond pdb=" CQ 4HH H 41 " pdb=" NR 4HH H 41 " ideal model delta sigma weight residual 1.374 1.452 -0.078 2.00e-02 2.50e+03 1.53e+01 bond pdb=" CQ 4HH G 41 " pdb=" NR 4HH G 41 " ideal model delta sigma weight residual 1.374 1.452 -0.078 2.00e-02 2.50e+03 1.53e+01 ... (remaining 19771 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.40: 26755 3.40 - 6.81: 128 6.81 - 10.21: 3 10.21 - 13.61: 6 13.61 - 17.01: 1 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 119.19 136.20 -17.01 3.00e+00 1.11e-01 3.22e+01 angle pdb=" O1P 4HH G 41 " pdb=" P 4HH G 41 " pdb=" O2P 4HH G 41 " ideal model delta sigma weight residual 122.75 109.29 13.46 3.00e+00 1.11e-01 2.01e+01 angle pdb=" O1P 4HH H 41 " pdb=" P 4HH H 41 " pdb=" O2P 4HH H 41 " ideal model delta sigma weight residual 122.75 109.33 13.42 3.00e+00 1.11e-01 2.00e+01 angle pdb=" O1P 4HH I 41 " pdb=" P 4HH I 41 " pdb=" O2P 4HH I 41 " ideal model delta sigma weight residual 122.75 109.63 13.12 3.00e+00 1.11e-01 1.91e+01 angle pdb=" OG 4HH I 41 " pdb=" P 4HH I 41 " pdb=" O3P 4HH I 41 " ideal model delta sigma weight residual 96.91 109.46 -12.55 3.00e+00 1.11e-01 1.75e+01 ... (remaining 26888 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.83: 11370 31.83 - 63.66: 368 63.66 - 95.48: 35 95.48 - 127.31: 1 127.31 - 159.14: 3 Dihedral angle restraints: 11777 sinusoidal: 4538 harmonic: 7239 Sorted by residual: dihedral pdb=" CQ 4HH I 41 " pdb=" CO 4HH I 41 " pdb=" CP 4HH I 41 " pdb=" NN 4HH I 41 " ideal model delta sinusoidal sigma weight residual 156.22 -44.64 -159.14 1 3.00e+01 1.11e-03 2.06e+01 dihedral pdb=" CQ 4HH H 41 " pdb=" CO 4HH H 41 " pdb=" CP 4HH H 41 " pdb=" NN 4HH H 41 " ideal model delta sinusoidal sigma weight residual 156.22 -61.16 -142.62 1 3.00e+01 1.11e-03 1.91e+01 dihedral pdb=" N L9Q A 101 " pdb=" C4 L9Q A 101 " pdb=" C5 L9Q A 101 " pdb=" O4P L9Q A 101 " ideal model delta sinusoidal sigma weight residual 291.48 149.15 142.33 1 3.00e+01 1.11e-03 1.91e+01 ... (remaining 11774 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 2479 0.049 - 0.099: 632 0.099 - 0.148: 113 0.148 - 0.197: 2 0.197 - 0.247: 1 Chirality restraints: 3227 Sorted by residual: chirality pdb=" CB VAL F 835 " pdb=" CA VAL F 835 " pdb=" CG1 VAL F 835 " pdb=" CG2 VAL F 835 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.25 2.00e-01 2.50e+01 1.52e+00 chirality pdb=" CA ILE D 948 " pdb=" N ILE D 948 " pdb=" C ILE D 948 " pdb=" CB ILE D 948 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.04e-01 chirality pdb=" CB THR D 42 " pdb=" CA THR D 42 " pdb=" OG1 THR D 42 " pdb=" CG2 THR D 42 " both_signs ideal model delta sigma weight residual False 2.55 2.40 0.15 2.00e-01 2.50e+01 5.62e-01 ... (remaining 3224 not shown) Planarity restraints: 3377 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TRP F 939 " 0.033 5.00e-02 4.00e+02 5.04e-02 4.06e+00 pdb=" N PRO F 940 " -0.087 5.00e-02 4.00e+02 pdb=" CA PRO F 940 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO F 940 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO F 692 " -0.033 5.00e-02 4.00e+02 4.99e-02 3.99e+00 pdb=" N PRO F 693 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO F 693 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO F 693 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE E 129 " -0.015 2.00e-02 2.50e+03 1.50e-02 3.95e+00 pdb=" CG PHE E 129 " 0.035 2.00e-02 2.50e+03 pdb=" CD1 PHE E 129 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 PHE E 129 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE E 129 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE E 129 " -0.004 2.00e-02 2.50e+03 pdb=" CZ PHE E 129 " -0.003 2.00e-02 2.50e+03 ... (remaining 3374 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 4284 2.79 - 3.31: 20125 3.31 - 3.84: 30700 3.84 - 4.37: 34115 4.37 - 4.90: 61019 Nonbonded interactions: 150243 Sorted by model distance: nonbonded pdb=" O GLN F 702 " pdb=" OE1 GLU F 706 " model vdw 2.257 3.040 nonbonded pdb=" O LEU I 37 " pdb=" OD1 ASP I 38 " model vdw 2.271 3.040 nonbonded pdb=" OD1 ASN F 867 " pdb=" OD2 ASP H 53 " model vdw 2.310 3.040 nonbonded pdb=" O2 L9Q B 101 " pdb=" O3 L9Q B 101 " model vdw 2.340 2.432 nonbonded pdb=" O ILE D 43 " pdb=" ND2 ASN D 47 " model vdw 2.349 3.120 ... (remaining 150238 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) selection = (chain 'B' and resid 1 through 31) selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = (chain 'F' and resid 20 through 952) } 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: 6.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 21.010 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 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 0.135 19776 Z= 0.225 Angle : 0.693 17.013 26893 Z= 0.351 Chirality : 0.044 0.247 3227 Planarity : 0.005 0.066 3377 Dihedral : 15.692 159.140 7129 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % 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: 0.76 (0.16), residues: 2516 helix: 1.17 (0.12), residues: 1670 sheet: 0.89 (0.43), residues: 135 loop : -1.10 (0.23), residues: 711 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG F 372 TYR 0.030 0.002 TYR G 55 PHE 0.035 0.002 PHE E 129 TRP 0.018 0.002 TRP E 952 HIS 0.010 0.001 HIS E 122 Details of bonding type rmsd covalent geometry : bond 0.00488 (19776) covalent geometry : angle 0.69344 (26893) hydrogen bonds : bond 0.12455 ( 1395) hydrogen bonds : angle 6.04081 ( 4143) *********************** 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 376 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 376 time to evaluate : 0.764 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 7 ARG cc_start: 0.8157 (mtp180) cc_final: 0.7879 (mmp-170) REVERT: B 10 ILE cc_start: 0.8978 (mt) cc_final: 0.8639 (mp) REVERT: B 14 ILE cc_start: 0.9443 (mp) cc_final: 0.9235 (mp) REVERT: B 27 ARG cc_start: 0.8908 (tpp-160) cc_final: 0.7402 (ttt180) REVERT: D 64 MET cc_start: 0.8606 (pmm) cc_final: 0.8306 (pmm) REVERT: D 352 THR cc_start: 0.8460 (m) cc_final: 0.8206 (p) REVERT: D 456 MET cc_start: 0.8728 (mmm) cc_final: 0.8527 (mtp) REVERT: D 775 ASP cc_start: 0.7963 (m-30) cc_final: 0.7758 (m-30) REVERT: F 775 ASP cc_start: 0.7690 (m-30) cc_final: 0.7433 (m-30) REVERT: F 874 MET cc_start: 0.8580 (mmm) cc_final: 0.8062 (mmt) REVERT: G 18 GLU cc_start: 0.8659 (tm-30) cc_final: 0.8398 (tm-30) REVERT: G 38 ASP cc_start: 0.8636 (t0) cc_final: 0.8417 (t0) REVERT: G 54 LYS cc_start: 0.8879 (tttt) cc_final: 0.8325 (tttt) REVERT: H 69 THR cc_start: 0.9374 (p) cc_final: 0.8866 (t) REVERT: I 17 GLU cc_start: 0.8147 (tp30) cc_final: 0.7519 (tp30) outliers start: 0 outliers final: 0 residues processed: 376 average time/residue: 0.1399 time to fit residues: 82.1236 Evaluate side-chains 289 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 289 time to evaluate : 0.718 ------------------------------------------------------------------------------- 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: 1.9990 chunk 98 optimal weight: 0.9980 chunk 194 optimal weight: 2.9990 chunk 227 optimal weight: 0.9980 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 0.9990 chunk 247 optimal weight: 2.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 60 GLN D 124 GLN D 286 GLN D 428 ASN D 444 ASN ** E 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 428 ASN I 78 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.085855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.069354 restraints weight = 52713.440| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 3.49 r_work: 0.2974 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.1304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 19776 Z= 0.147 Angle : 0.621 10.034 26893 Z= 0.316 Chirality : 0.043 0.195 3227 Planarity : 0.005 0.040 3377 Dihedral : 9.642 161.894 2845 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.83 % Allowed : 10.40 % Favored : 87.77 % 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: 1.36 (0.17), residues: 2516 helix: 1.59 (0.12), residues: 1688 sheet: 1.48 (0.45), residues: 132 loop : -0.89 (0.23), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 224 TYR 0.015 0.002 TYR E 331 PHE 0.018 0.001 PHE E 129 TRP 0.012 0.001 TRP F 833 HIS 0.004 0.001 HIS D 77 Details of bonding type rmsd covalent geometry : bond 0.00319 (19776) covalent geometry : angle 0.62081 (26893) hydrogen bonds : bond 0.05342 ( 1395) hydrogen bonds : angle 4.74598 ( 4143) *********************** 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: 37 poor density : 307 time to evaluate : 0.769 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 6 LYS cc_start: 0.7181 (mmtp) cc_final: 0.6886 (mmtt) REVERT: B 7 ARG cc_start: 0.8027 (mtp180) cc_final: 0.7586 (mmp-170) REVERT: B 15 LEU cc_start: 0.9413 (OUTLIER) cc_final: 0.9174 (mm) REVERT: B 27 ARG cc_start: 0.8747 (tpp-160) cc_final: 0.7043 (ttt180) REVERT: D 54 GLU cc_start: 0.7731 (pt0) cc_final: 0.7522 (mp0) REVERT: D 72 MET cc_start: 0.9059 (tpp) cc_final: 0.8800 (tpp) REVERT: D 92 MET cc_start: 0.8902 (mmt) cc_final: 0.8391 (mmt) REVERT: D 183 LYS cc_start: 0.7707 (ptpt) cc_final: 0.7310 (ptmt) REVERT: D 205 GLN cc_start: 0.9269 (mt0) cc_final: 0.9062 (tp40) REVERT: D 352 THR cc_start: 0.8090 (m) cc_final: 0.7664 (p) REVERT: D 777 MET cc_start: 0.8945 (OUTLIER) cc_final: 0.8676 (ptp) REVERT: F 775 ASP cc_start: 0.8433 (m-30) cc_final: 0.8232 (m-30) REVERT: F 874 MET cc_start: 0.8562 (mmm) cc_final: 0.8037 (mmt) REVERT: H 14 GLU cc_start: 0.8701 (mt-10) cc_final: 0.8357 (mp0) REVERT: H 30 GLU cc_start: 0.8759 (OUTLIER) cc_final: 0.8448 (pm20) REVERT: I 17 GLU cc_start: 0.8491 (tp30) cc_final: 0.8197 (tp30) REVERT: I 46 GLU cc_start: 0.7406 (mt-10) cc_final: 0.7166 (mt-10) outliers start: 37 outliers final: 17 residues processed: 326 average time/residue: 0.1426 time to fit residues: 72.4706 Evaluate side-chains 303 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 283 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 344 VAL Chi-restraints excluded: chain D residue 407 THR Chi-restraints excluded: chain D residue 777 MET Chi-restraints excluded: chain D residue 915 LEU Chi-restraints excluded: chain D residue 917 ASP Chi-restraints excluded: chain E residue 204 LEU Chi-restraints excluded: chain E residue 323 CYS Chi-restraints excluded: chain E residue 405 LEU Chi-restraints excluded: chain E residue 431 TYR Chi-restraints excluded: chain E residue 894 SER Chi-restraints excluded: chain F residue 833 TRP Chi-restraints excluded: chain F residue 835 VAL Chi-restraints excluded: chain F residue 867 ASN Chi-restraints excluded: chain H residue 17 GLU Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 30 GLU Chi-restraints excluded: chain H residue 45 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 26 optimal weight: 7.9990 chunk 38 optimal weight: 2.9990 chunk 228 optimal weight: 6.9990 chunk 161 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 chunk 79 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 233 optimal weight: 0.8980 chunk 133 optimal weight: 0.9980 chunk 217 optimal weight: 0.7980 chunk 110 optimal weight: 1.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 124 GLN ** E 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 832 HIS F 163 ASN H 78 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.085724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.069269 restraints weight = 52915.035| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 3.50 r_work: 0.2973 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.1626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 19776 Z= 0.142 Angle : 0.579 8.659 26893 Z= 0.295 Chirality : 0.042 0.167 3227 Planarity : 0.004 0.038 3377 Dihedral : 9.298 162.626 2845 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.67 % Allowed : 12.73 % Favored : 84.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.62 (0.17), residues: 2516 helix: 1.75 (0.12), residues: 1688 sheet: 1.76 (0.44), residues: 132 loop : -0.72 (0.23), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 68 TYR 0.014 0.001 TYR D 690 PHE 0.014 0.001 PHE E 129 TRP 0.012 0.001 TRP D 833 HIS 0.003 0.001 HIS F 722 Details of bonding type rmsd covalent geometry : bond 0.00319 (19776) covalent geometry : angle 0.57854 (26893) hydrogen bonds : bond 0.04925 ( 1395) hydrogen bonds : angle 4.47066 ( 4143) *********************** 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 361 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 307 time to evaluate : 0.741 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 LYS cc_start: 0.7322 (mmtp) cc_final: 0.7045 (mmtt) REVERT: B 7 ARG cc_start: 0.7996 (mtp180) cc_final: 0.7578 (mmp-170) REVERT: B 15 LEU cc_start: 0.9393 (OUTLIER) cc_final: 0.9061 (mm) REVERT: B 27 ARG cc_start: 0.8768 (tpp-160) cc_final: 0.7106 (ttt180) REVERT: D 64 MET cc_start: 0.8823 (pmm) cc_final: 0.8487 (pmm) REVERT: D 92 MET cc_start: 0.8810 (mmt) cc_final: 0.8407 (mpp) REVERT: D 208 GLU cc_start: 0.8282 (tm-30) cc_final: 0.8039 (tm-30) REVERT: D 352 THR cc_start: 0.8103 (m) cc_final: 0.7658 (p) REVERT: D 449 MET cc_start: 0.8971 (ttt) cc_final: 0.8544 (ttt) REVERT: D 777 MET cc_start: 0.8955 (OUTLIER) cc_final: 0.8690 (ptp) REVERT: E 27 MET cc_start: 0.7854 (tmm) cc_final: 0.7635 (tmm) REVERT: E 412 ARG cc_start: 0.8926 (mmm-85) cc_final: 0.8410 (mmp80) REVERT: F 357 ILE cc_start: 0.6861 (OUTLIER) cc_final: 0.6627 (pt) REVERT: F 775 ASP cc_start: 0.8410 (m-30) cc_final: 0.8209 (m-30) REVERT: F 791 MET cc_start: 0.9172 (tpp) cc_final: 0.8967 (mmm) REVERT: F 874 MET cc_start: 0.8621 (mmm) cc_final: 0.8162 (mmt) REVERT: G 54 LYS cc_start: 0.8552 (tttt) cc_final: 0.8344 (ttmt) REVERT: I 17 GLU cc_start: 0.8479 (tp30) cc_final: 0.7530 (tp30) REVERT: I 18 GLU cc_start: 0.9284 (tt0) cc_final: 0.8928 (tp30) REVERT: I 46 GLU cc_start: 0.7459 (mt-10) cc_final: 0.7085 (mt-10) outliers start: 54 outliers final: 28 residues processed: 335 average time/residue: 0.1393 time to fit residues: 73.0467 Evaluate side-chains 314 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 283 time to evaluate : 0.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 54 GLU Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 344 VAL Chi-restraints excluded: chain D residue 407 THR Chi-restraints excluded: chain D residue 417 ASP Chi-restraints excluded: chain D residue 777 MET Chi-restraints excluded: chain D residue 915 LEU Chi-restraints excluded: chain D residue 917 ASP Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain E residue 204 LEU Chi-restraints excluded: chain E residue 323 CYS Chi-restraints excluded: chain E residue 405 LEU Chi-restraints excluded: chain E residue 431 TYR Chi-restraints excluded: chain E residue 894 SER Chi-restraints excluded: chain F residue 271 ILE Chi-restraints excluded: chain F residue 357 ILE Chi-restraints excluded: chain F residue 406 LEU Chi-restraints excluded: chain F residue 833 TRP Chi-restraints excluded: chain F residue 835 VAL Chi-restraints excluded: chain F residue 862 ILE Chi-restraints excluded: chain F residue 867 ASN Chi-restraints excluded: chain F residue 914 LEU Chi-restraints excluded: chain F residue 942 VAL Chi-restraints excluded: chain H residue 30 GLU Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 78 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 51 optimal weight: 0.7980 chunk 215 optimal weight: 2.9990 chunk 229 optimal weight: 2.9990 chunk 36 optimal weight: 0.3980 chunk 14 optimal weight: 0.3980 chunk 3 optimal weight: 10.0000 chunk 68 optimal weight: 3.9990 chunk 91 optimal weight: 3.9990 chunk 17 optimal weight: 8.9990 chunk 6 optimal weight: 10.0000 chunk 226 optimal weight: 0.7980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 286 GLN E 122 HIS ** E 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 832 HIS H 78 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.085749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.069290 restraints weight = 53367.714| |-----------------------------------------------------------------------------| r_work (start): 0.3107 rms_B_bonded: 3.51 r_work: 0.2974 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.1844 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= 0.138 Angle : 0.577 12.701 26893 Z= 0.291 Chirality : 0.042 0.325 3227 Planarity : 0.004 0.042 3377 Dihedral : 9.098 162.631 2845 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.97 % Allowed : 14.61 % Favored : 82.42 % 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: 1.75 (0.17), residues: 2516 helix: 1.84 (0.12), residues: 1688 sheet: 1.81 (0.44), residues: 132 loop : -0.63 (0.24), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 68 TYR 0.009 0.001 TYR D 223 PHE 0.033 0.001 PHE F 888 TRP 0.011 0.001 TRP F 833 HIS 0.003 0.001 HIS F 722 Details of bonding type rmsd covalent geometry : bond 0.00310 (19776) covalent geometry : angle 0.57665 (26893) hydrogen bonds : bond 0.04740 ( 1395) hydrogen bonds : angle 4.35364 ( 4143) *********************** 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 362 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 302 time to evaluate : 0.698 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 LYS cc_start: 0.7352 (mmtp) cc_final: 0.7092 (mmtt) REVERT: B 15 LEU cc_start: 0.9332 (OUTLIER) cc_final: 0.9070 (mm) REVERT: B 27 ARG cc_start: 0.8807 (tpp-160) cc_final: 0.7104 (ttt180) REVERT: D 64 MET cc_start: 0.8853 (pmm) cc_final: 0.8510 (pmm) REVERT: D 92 MET cc_start: 0.8790 (mmt) cc_final: 0.8478 (mpp) REVERT: D 352 THR cc_start: 0.8128 (m) cc_final: 0.7674 (p) REVERT: D 429 GLU cc_start: 0.8251 (OUTLIER) cc_final: 0.7955 (mp0) REVERT: D 449 MET cc_start: 0.9099 (ttt) cc_final: 0.8636 (ttt) REVERT: D 777 MET cc_start: 0.8973 (OUTLIER) cc_final: 0.8711 (ptp) REVERT: E 27 MET cc_start: 0.7863 (tmm) cc_final: 0.7590 (tmm) REVERT: E 195 ASP cc_start: 0.9189 (OUTLIER) cc_final: 0.8646 (t0) REVERT: F 357 ILE cc_start: 0.6863 (OUTLIER) cc_final: 0.6657 (pt) REVERT: F 775 ASP cc_start: 0.8405 (m-30) cc_final: 0.8203 (m-30) REVERT: F 874 MET cc_start: 0.8599 (mmm) cc_final: 0.8232 (mmt) REVERT: G 30 GLU cc_start: 0.8709 (pp20) cc_final: 0.8177 (mp0) REVERT: G 54 LYS cc_start: 0.8453 (tttt) cc_final: 0.8242 (ttmt) REVERT: H 14 GLU cc_start: 0.8889 (mt-10) cc_final: 0.8625 (mp0) REVERT: I 17 GLU cc_start: 0.8511 (tp30) cc_final: 0.8263 (tp30) REVERT: I 18 GLU cc_start: 0.9258 (tt0) cc_final: 0.8900 (tp30) outliers start: 60 outliers final: 37 residues processed: 333 average time/residue: 0.1364 time to fit residues: 71.6676 Evaluate side-chains 324 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 282 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain D residue 24 ILE Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 187 THR Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 302 MET Chi-restraints excluded: chain D residue 344 VAL Chi-restraints excluded: chain D residue 407 THR Chi-restraints excluded: chain D residue 417 ASP Chi-restraints excluded: chain D residue 429 GLU Chi-restraints excluded: chain D residue 777 MET Chi-restraints excluded: chain D residue 915 LEU Chi-restraints excluded: chain D residue 917 ASP Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain E residue 195 ASP Chi-restraints excluded: chain E residue 204 LEU Chi-restraints excluded: chain E residue 323 CYS Chi-restraints excluded: chain E residue 405 LEU Chi-restraints excluded: chain E residue 431 TYR Chi-restraints excluded: chain E residue 894 SER Chi-restraints excluded: chain E residue 928 SER Chi-restraints excluded: chain F residue 120 THR Chi-restraints excluded: chain F residue 357 ILE Chi-restraints excluded: chain F residue 406 LEU Chi-restraints excluded: chain F residue 786 LEU Chi-restraints excluded: chain F residue 833 TRP Chi-restraints excluded: chain F residue 835 VAL Chi-restraints excluded: chain F residue 852 LEU Chi-restraints excluded: chain F residue 862 ILE Chi-restraints excluded: chain F residue 867 ASN Chi-restraints excluded: chain F residue 919 LEU Chi-restraints excluded: chain F residue 942 VAL Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain G residue 61 ASP Chi-restraints excluded: chain H residue 17 GLU Chi-restraints excluded: chain H residue 30 GLU Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain I residue 58 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 211 optimal weight: 3.9990 chunk 39 optimal weight: 0.0970 chunk 65 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 chunk 60 optimal weight: 0.1980 chunk 169 optimal weight: 0.9990 chunk 47 optimal weight: 6.9990 chunk 212 optimal weight: 1.9990 chunk 6 optimal weight: 10.0000 chunk 28 optimal weight: 3.9990 chunk 29 optimal weight: 0.7980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 26 GLN D 286 GLN ** E 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 78 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.086925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.070717 restraints weight = 52509.511| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 3.47 r_work: 0.3005 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.2096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 19776 Z= 0.120 Angle : 0.560 9.929 26893 Z= 0.283 Chirality : 0.042 0.184 3227 Planarity : 0.004 0.042 3377 Dihedral : 8.842 160.477 2845 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.67 % Allowed : 16.25 % Favored : 81.08 % 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: 1.91 (0.12), residues: 1697 sheet: 1.50 (0.45), residues: 147 loop : -0.53 (0.24), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 68 TYR 0.015 0.001 TYR D 690 PHE 0.019 0.001 PHE F 888 TRP 0.010 0.001 TRP F 833 HIS 0.003 0.000 HIS E 122 Details of bonding type rmsd covalent geometry : bond 0.00256 (19776) covalent geometry : angle 0.55952 (26893) hydrogen bonds : bond 0.04409 ( 1395) hydrogen bonds : angle 4.25823 ( 4143) *********************** 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 360 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 306 time to evaluate : 0.812 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 7 ARG cc_start: 0.8138 (mtp-110) cc_final: 0.7591 (mmp-170) REVERT: B 15 LEU cc_start: 0.9336 (OUTLIER) cc_final: 0.9096 (mm) REVERT: B 27 ARG cc_start: 0.8755 (tpp-160) cc_final: 0.7065 (ttt180) REVERT: D 23 PHE cc_start: 0.7293 (t80) cc_final: 0.7047 (t80) REVERT: D 64 MET cc_start: 0.8845 (pmm) cc_final: 0.8508 (pmm) REVERT: D 92 MET cc_start: 0.8763 (mmt) cc_final: 0.8414 (mpp) REVERT: D 327 THR cc_start: 0.6713 (OUTLIER) cc_final: 0.6211 (t) REVERT: D 429 GLU cc_start: 0.8242 (OUTLIER) cc_final: 0.7989 (mp0) REVERT: D 449 MET cc_start: 0.9109 (ttt) cc_final: 0.8655 (ttt) REVERT: D 777 MET cc_start: 0.8977 (OUTLIER) cc_final: 0.8732 (ptp) REVERT: D 917 ASP cc_start: 0.8596 (OUTLIER) cc_final: 0.8313 (m-30) REVERT: E 27 MET cc_start: 0.7839 (tmm) cc_final: 0.7234 (tmm) REVERT: E 195 ASP cc_start: 0.9145 (OUTLIER) cc_final: 0.8611 (t0) REVERT: E 405 LEU cc_start: 0.8830 (OUTLIER) cc_final: 0.8548 (mt) REVERT: E 412 ARG cc_start: 0.8930 (mmm-85) cc_final: 0.8419 (mmp80) REVERT: E 892 MET cc_start: 0.8784 (tpp) cc_final: 0.8403 (mmm) REVERT: F 775 ASP cc_start: 0.8341 (m-30) cc_final: 0.8111 (m-30) REVERT: G 30 GLU cc_start: 0.8739 (pp20) cc_final: 0.8200 (mp0) REVERT: G 54 LYS cc_start: 0.8385 (tttt) cc_final: 0.8172 (ttmt) REVERT: H 18 GLU cc_start: 0.8829 (tt0) cc_final: 0.8535 (tm-30) REVERT: I 17 GLU cc_start: 0.8523 (tp30) cc_final: 0.8293 (tp30) REVERT: I 18 GLU cc_start: 0.9263 (tt0) cc_final: 0.8917 (tp30) REVERT: I 44 MET cc_start: 0.7222 (tmm) cc_final: 0.6880 (tmm) outliers start: 54 outliers final: 27 residues processed: 333 average time/residue: 0.1311 time to fit residues: 69.9234 Evaluate side-chains 307 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 273 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain D residue 187 THR Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 302 MET Chi-restraints excluded: chain D residue 327 THR Chi-restraints excluded: chain D residue 417 ASP Chi-restraints excluded: chain D residue 429 GLU Chi-restraints excluded: chain D residue 777 MET Chi-restraints excluded: chain D residue 915 LEU Chi-restraints excluded: chain D residue 917 ASP Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain E residue 195 ASP Chi-restraints excluded: chain E residue 204 LEU Chi-restraints excluded: chain E residue 323 CYS Chi-restraints excluded: chain E residue 405 LEU Chi-restraints excluded: chain E residue 894 SER Chi-restraints excluded: chain F residue 120 THR Chi-restraints excluded: chain F residue 406 LEU Chi-restraints excluded: chain F residue 833 TRP Chi-restraints excluded: chain F residue 835 VAL Chi-restraints excluded: chain F residue 852 LEU Chi-restraints excluded: chain F residue 862 ILE Chi-restraints excluded: chain F residue 867 ASN Chi-restraints excluded: chain F residue 914 LEU Chi-restraints excluded: chain F residue 942 VAL Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain H residue 17 GLU Chi-restraints excluded: chain H residue 30 GLU Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 78 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 95 optimal weight: 0.9980 chunk 26 optimal weight: 4.9990 chunk 47 optimal weight: 6.9990 chunk 177 optimal weight: 6.9990 chunk 236 optimal weight: 1.9990 chunk 106 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 52 optimal weight: 5.9990 chunk 148 optimal weight: 5.9990 chunk 211 optimal weight: 3.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 124 GLN ** D 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 286 GLN ** E 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 106 HIS I 78 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.084848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.068442 restraints weight = 53185.600| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 3.49 r_work: 0.2961 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.2100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 19776 Z= 0.177 Angle : 0.593 9.139 26893 Z= 0.304 Chirality : 0.044 0.229 3227 Planarity : 0.004 0.040 3377 Dihedral : 8.855 165.031 2845 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 3.22 % Allowed : 17.93 % Favored : 78.85 % 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: 1.82 (0.17), residues: 2516 helix: 1.86 (0.12), residues: 1694 sheet: 1.63 (0.45), residues: 132 loop : -0.51 (0.24), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 68 TYR 0.013 0.001 TYR D 223 PHE 0.020 0.001 PHE F 888 TRP 0.009 0.001 TRP F 833 HIS 0.004 0.001 HIS F 832 Details of bonding type rmsd covalent geometry : bond 0.00417 (19776) covalent geometry : angle 0.59327 (26893) hydrogen bonds : bond 0.04809 ( 1395) hydrogen bonds : angle 4.34427 ( 4143) *********************** 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 355 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 290 time to evaluate : 0.629 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 LYS cc_start: 0.7320 (mmtp) cc_final: 0.7071 (mmtt) REVERT: B 7 ARG cc_start: 0.8124 (mtp-110) cc_final: 0.7647 (mmp-170) REVERT: B 27 ARG cc_start: 0.8867 (tpp-160) cc_final: 0.7195 (ttt180) REVERT: D 64 MET cc_start: 0.8909 (pmm) cc_final: 0.8684 (pmm) REVERT: D 92 MET cc_start: 0.8755 (mmt) cc_final: 0.8325 (mpp) REVERT: D 176 LEU cc_start: 0.8510 (OUTLIER) cc_final: 0.8271 (tt) REVERT: D 208 GLU cc_start: 0.8351 (pp20) cc_final: 0.8049 (tm-30) REVERT: D 218 MET cc_start: 0.9189 (tpt) cc_final: 0.8886 (tpp) REVERT: D 327 THR cc_start: 0.6873 (OUTLIER) cc_final: 0.6264 (t) REVERT: D 429 GLU cc_start: 0.8232 (OUTLIER) cc_final: 0.7964 (mp0) REVERT: D 449 MET cc_start: 0.9154 (ttt) cc_final: 0.8734 (ttt) REVERT: D 777 MET cc_start: 0.8994 (OUTLIER) cc_final: 0.8748 (ptp) REVERT: E 27 MET cc_start: 0.7905 (tmm) cc_final: 0.7258 (tmm) REVERT: E 176 LEU cc_start: 0.6886 (OUTLIER) cc_final: 0.6494 (tt) REVERT: E 195 ASP cc_start: 0.9176 (OUTLIER) cc_final: 0.8655 (t0) REVERT: E 218 MET cc_start: 0.8709 (tpp) cc_final: 0.8386 (tpp) REVERT: E 405 LEU cc_start: 0.8850 (OUTLIER) cc_final: 0.8554 (mt) REVERT: F 449 MET cc_start: 0.8077 (ttp) cc_final: 0.7867 (ttp) REVERT: F 775 ASP cc_start: 0.8397 (m-30) cc_final: 0.8178 (m-30) REVERT: G 30 GLU cc_start: 0.8787 (pp20) cc_final: 0.8193 (mp0) REVERT: G 54 LYS cc_start: 0.8406 (tttt) cc_final: 0.8103 (ttmm) REVERT: I 17 GLU cc_start: 0.8557 (tp30) cc_final: 0.8291 (tp30) REVERT: I 18 GLU cc_start: 0.9263 (tt0) cc_final: 0.8967 (tp30) REVERT: I 44 MET cc_start: 0.7276 (tmm) cc_final: 0.6897 (tmm) outliers start: 65 outliers final: 36 residues processed: 325 average time/residue: 0.1236 time to fit residues: 64.2880 Evaluate side-chains 317 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 274 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain D residue 24 ILE Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 187 THR Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 302 MET Chi-restraints excluded: chain D residue 327 THR Chi-restraints excluded: chain D residue 407 THR Chi-restraints excluded: chain D residue 417 ASP Chi-restraints excluded: chain D residue 429 GLU Chi-restraints excluded: chain D residue 777 MET Chi-restraints excluded: chain D residue 902 VAL Chi-restraints excluded: chain D residue 915 LEU Chi-restraints excluded: chain D residue 917 ASP Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain E residue 135 THR Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 195 ASP Chi-restraints excluded: chain E residue 204 LEU Chi-restraints excluded: chain E residue 291 LEU Chi-restraints excluded: chain E residue 323 CYS Chi-restraints excluded: chain E residue 405 LEU Chi-restraints excluded: chain E residue 840 VAL Chi-restraints excluded: chain E residue 894 SER Chi-restraints excluded: chain E residue 928 SER Chi-restraints excluded: chain F residue 120 THR Chi-restraints excluded: chain F residue 406 LEU Chi-restraints excluded: chain F residue 786 LEU Chi-restraints excluded: chain F residue 833 TRP Chi-restraints excluded: chain F residue 835 VAL Chi-restraints excluded: chain F residue 852 LEU Chi-restraints excluded: chain F residue 862 ILE Chi-restraints excluded: chain F residue 867 ASN Chi-restraints excluded: chain F residue 914 LEU Chi-restraints excluded: chain F residue 942 VAL Chi-restraints excluded: chain G residue 40 ASP Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain G residue 61 ASP Chi-restraints excluded: chain H residue 17 GLU Chi-restraints excluded: chain H residue 42 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 128 optimal weight: 0.0050 chunk 8 optimal weight: 0.9990 chunk 31 optimal weight: 6.9990 chunk 200 optimal weight: 0.0770 chunk 188 optimal weight: 0.6980 chunk 248 optimal weight: 0.0670 chunk 100 optimal weight: 5.9990 chunk 233 optimal weight: 3.9990 chunk 238 optimal weight: 5.9990 chunk 67 optimal weight: 1.9990 chunk 158 optimal weight: 4.9990 overall best weight: 0.3692 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 286 GLN E 58 GLN ** E 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 78 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.088044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.071898 restraints weight = 52264.002| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 3.49 r_work: 0.3015 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.2371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 19776 Z= 0.119 Angle : 0.580 13.321 26893 Z= 0.290 Chirality : 0.043 0.372 3227 Planarity : 0.004 0.041 3377 Dihedral : 8.598 159.166 2845 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.58 % Allowed : 18.92 % Favored : 78.50 % 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: 1.94 (0.17), residues: 2516 helix: 1.95 (0.12), residues: 1709 sheet: 1.50 (0.45), residues: 147 loop : -0.50 (0.24), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 412 TYR 0.019 0.001 TYR D 690 PHE 0.021 0.001 PHE D 23 TRP 0.009 0.001 TRP E 379 HIS 0.003 0.001 HIS F 454 Details of bonding type rmsd covalent geometry : bond 0.00244 (19776) covalent geometry : angle 0.57964 (26893) hydrogen bonds : bond 0.04244 ( 1395) hydrogen bonds : angle 4.23601 ( 4143) *********************** 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 361 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 309 time to evaluate : 0.772 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 7 ARG cc_start: 0.8096 (mtp-110) cc_final: 0.7614 (mmp-170) REVERT: B 27 ARG cc_start: 0.8761 (tpp-160) cc_final: 0.7093 (ttt180) REVERT: D 23 PHE cc_start: 0.6957 (t80) cc_final: 0.6613 (t80) REVERT: D 92 MET cc_start: 0.8729 (mmt) cc_final: 0.8388 (mpp) REVERT: D 176 LEU cc_start: 0.8482 (OUTLIER) cc_final: 0.8244 (tt) REVERT: D 218 MET cc_start: 0.9147 (tpt) cc_final: 0.8859 (tpp) REVERT: D 327 THR cc_start: 0.6460 (OUTLIER) cc_final: 0.5963 (t) REVERT: D 429 GLU cc_start: 0.8258 (OUTLIER) cc_final: 0.7989 (mp0) REVERT: D 449 MET cc_start: 0.9150 (ttt) cc_final: 0.8718 (ttt) REVERT: D 777 MET cc_start: 0.8908 (ptm) cc_final: 0.8599 (ptp) REVERT: D 917 ASP cc_start: 0.8591 (OUTLIER) cc_final: 0.8321 (m-30) REVERT: E 27 MET cc_start: 0.7806 (tmm) cc_final: 0.7188 (tmm) REVERT: E 195 ASP cc_start: 0.9176 (OUTLIER) cc_final: 0.8670 (t0) REVERT: E 412 ARG cc_start: 0.8944 (mmm-85) cc_final: 0.8453 (mmp80) REVERT: E 892 MET cc_start: 0.8732 (tpp) cc_final: 0.8400 (mmm) REVERT: F 775 ASP cc_start: 0.8407 (m-30) cc_final: 0.8159 (m-30) REVERT: G 30 GLU cc_start: 0.8798 (pp20) cc_final: 0.8210 (mp0) REVERT: G 54 LYS cc_start: 0.8288 (tttt) cc_final: 0.7939 (ttmm) REVERT: H 14 GLU cc_start: 0.8841 (mt-10) cc_final: 0.8535 (mp0) REVERT: H 18 GLU cc_start: 0.8759 (tt0) cc_final: 0.8463 (tm-30) REVERT: I 17 GLU cc_start: 0.8537 (tp30) cc_final: 0.8274 (tp30) REVERT: I 18 GLU cc_start: 0.9322 (tt0) cc_final: 0.9011 (tp30) REVERT: I 44 MET cc_start: 0.7084 (tmm) cc_final: 0.6740 (tmm) outliers start: 52 outliers final: 30 residues processed: 338 average time/residue: 0.1316 time to fit residues: 70.9029 Evaluate side-chains 317 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 282 time to evaluate : 0.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 54 GLU Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 187 THR Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 302 MET Chi-restraints excluded: chain D residue 327 THR Chi-restraints excluded: chain D residue 387 VAL Chi-restraints excluded: chain D residue 429 GLU Chi-restraints excluded: chain D residue 915 LEU Chi-restraints excluded: chain D residue 917 ASP Chi-restraints excluded: chain E residue 58 GLN Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain E residue 195 ASP Chi-restraints excluded: chain E residue 204 LEU Chi-restraints excluded: chain E residue 323 CYS Chi-restraints excluded: chain E residue 832 HIS Chi-restraints excluded: chain E residue 833 TRP Chi-restraints excluded: chain E residue 840 VAL Chi-restraints excluded: chain E residue 928 SER Chi-restraints excluded: chain F residue 406 LEU Chi-restraints excluded: chain F residue 833 TRP Chi-restraints excluded: chain F residue 835 VAL Chi-restraints excluded: chain F residue 867 ASN Chi-restraints excluded: chain F residue 914 LEU Chi-restraints excluded: chain F residue 942 VAL Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain H residue 17 GLU Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 78 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 222 optimal weight: 0.8980 chunk 195 optimal weight: 0.9990 chunk 13 optimal weight: 0.8980 chunk 171 optimal weight: 0.0170 chunk 88 optimal weight: 0.9980 chunk 91 optimal weight: 4.9990 chunk 37 optimal weight: 3.9990 chunk 96 optimal weight: 0.9990 chunk 148 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 12 optimal weight: 0.0020 overall best weight: 0.5626 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 286 GLN ** E 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 78 GLN ** 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 = 0.3460 r_free = 0.3460 target = 0.087956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.071568 restraints weight = 52161.140| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 3.52 r_work: 0.3011 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.2464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 19776 Z= 0.120 Angle : 0.584 8.619 26893 Z= 0.293 Chirality : 0.043 0.351 3227 Planarity : 0.004 0.039 3377 Dihedral : 8.490 160.054 2845 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.67 % Allowed : 19.76 % Favored : 77.56 % 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: 2.04 (0.17), residues: 2516 helix: 2.04 (0.12), residues: 1694 sheet: 1.56 (0.45), residues: 147 loop : -0.46 (0.24), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 68 TYR 0.014 0.001 TYR D 223 PHE 0.016 0.001 PHE D 23 TRP 0.010 0.001 TRP E 379 HIS 0.003 0.000 HIS E 122 Details of bonding type rmsd covalent geometry : bond 0.00259 (19776) covalent geometry : angle 0.58402 (26893) hydrogen bonds : bond 0.04210 ( 1395) hydrogen bonds : angle 4.24255 ( 4143) *********************** 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 357 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 303 time to evaluate : 0.764 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 7 ARG cc_start: 0.8105 (mtp-110) cc_final: 0.7629 (mmp-170) REVERT: B 27 ARG cc_start: 0.8794 (tpp-160) cc_final: 0.7145 (ttt180) REVERT: D 23 PHE cc_start: 0.6922 (t80) cc_final: 0.6702 (t80) REVERT: D 64 MET cc_start: 0.8879 (pmm) cc_final: 0.8502 (pmm) REVERT: D 92 MET cc_start: 0.8712 (mmt) cc_final: 0.8401 (mpp) REVERT: D 176 LEU cc_start: 0.8472 (OUTLIER) cc_final: 0.8230 (tt) REVERT: D 218 MET cc_start: 0.9145 (tpt) cc_final: 0.8854 (tpp) REVERT: D 327 THR cc_start: 0.6504 (OUTLIER) cc_final: 0.6024 (t) REVERT: D 429 GLU cc_start: 0.8268 (OUTLIER) cc_final: 0.8006 (mp0) REVERT: D 449 MET cc_start: 0.9200 (ttt) cc_final: 0.8794 (ttt) REVERT: D 917 ASP cc_start: 0.8594 (OUTLIER) cc_final: 0.8316 (m-30) REVERT: E 27 MET cc_start: 0.7815 (tmm) cc_final: 0.7202 (tmm) REVERT: E 195 ASP cc_start: 0.9200 (OUTLIER) cc_final: 0.8722 (t0) REVERT: E 412 ARG cc_start: 0.8958 (mmm-85) cc_final: 0.8440 (mmp80) REVERT: E 892 MET cc_start: 0.8755 (tpp) cc_final: 0.8258 (mmm) REVERT: F 449 MET cc_start: 0.7971 (ttp) cc_final: 0.7709 (ttp) REVERT: F 775 ASP cc_start: 0.8402 (m-30) cc_final: 0.8143 (m-30) REVERT: F 868 THR cc_start: 0.9122 (OUTLIER) cc_final: 0.8871 (m) REVERT: G 30 GLU cc_start: 0.8793 (pp20) cc_final: 0.8207 (mp0) REVERT: G 54 LYS cc_start: 0.8303 (tttt) cc_final: 0.8092 (ttmt) REVERT: H 14 GLU cc_start: 0.8813 (mt-10) cc_final: 0.8522 (mp0) REVERT: H 18 GLU cc_start: 0.8713 (tt0) cc_final: 0.8454 (tm-30) REVERT: I 17 GLU cc_start: 0.8551 (tp30) cc_final: 0.8252 (tp30) REVERT: I 18 GLU cc_start: 0.9320 (tt0) cc_final: 0.9006 (tp30) REVERT: I 44 MET cc_start: 0.7119 (tmm) cc_final: 0.6783 (tmm) outliers start: 54 outliers final: 32 residues processed: 332 average time/residue: 0.1373 time to fit residues: 72.4577 Evaluate side-chains 333 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 295 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 54 GLU Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 187 THR Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 302 MET Chi-restraints excluded: chain D residue 327 THR Chi-restraints excluded: chain D residue 387 VAL Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain D residue 429 GLU Chi-restraints excluded: chain D residue 902 VAL Chi-restraints excluded: chain D residue 915 LEU Chi-restraints excluded: chain D residue 917 ASP Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain E residue 195 ASP Chi-restraints excluded: chain E residue 204 LEU Chi-restraints excluded: chain E residue 323 CYS Chi-restraints excluded: chain E residue 833 TRP Chi-restraints excluded: chain E residue 840 VAL Chi-restraints excluded: chain E residue 928 SER Chi-restraints excluded: chain F residue 406 LEU Chi-restraints excluded: chain F residue 833 TRP Chi-restraints excluded: chain F residue 835 VAL Chi-restraints excluded: chain F residue 852 LEU Chi-restraints excluded: chain F residue 867 ASN Chi-restraints excluded: chain F residue 868 THR Chi-restraints excluded: chain F residue 914 LEU Chi-restraints excluded: chain F residue 942 VAL Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain H residue 17 GLU Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain I residue 58 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 57 optimal weight: 0.2980 chunk 125 optimal weight: 2.9990 chunk 144 optimal weight: 0.7980 chunk 85 optimal weight: 0.9990 chunk 95 optimal weight: 0.0870 chunk 40 optimal weight: 0.4980 chunk 200 optimal weight: 0.6980 chunk 218 optimal weight: 2.9990 chunk 82 optimal weight: 0.0020 chunk 133 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 overall best weight: 0.3166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 286 GLN ** E 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 832 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.088950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.072858 restraints weight = 52134.020| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 3.50 r_work: 0.3034 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.2640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.068 19776 Z= 0.118 Angle : 0.599 9.767 26893 Z= 0.298 Chirality : 0.043 0.284 3227 Planarity : 0.004 0.040 3377 Dihedral : 8.310 158.320 2845 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.13 % Allowed : 20.26 % Favored : 77.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.07 (0.17), residues: 2516 helix: 2.04 (0.12), residues: 1697 sheet: 1.55 (0.45), residues: 147 loop : -0.40 (0.24), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 99 TYR 0.020 0.001 TYR D 690 PHE 0.016 0.001 PHE D 23 TRP 0.012 0.001 TRP E 379 HIS 0.005 0.000 HIS F 722 Details of bonding type rmsd covalent geometry : bond 0.00246 (19776) covalent geometry : angle 0.59861 (26893) hydrogen bonds : bond 0.04012 ( 1395) hydrogen bonds : angle 4.22293 ( 4143) *********************** 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 361 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 318 time to evaluate : 0.722 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 7 ARG cc_start: 0.8131 (mtp-110) cc_final: 0.7641 (mmp-170) REVERT: B 27 ARG cc_start: 0.8784 (tpp-160) cc_final: 0.7137 (ttt180) REVERT: D 23 PHE cc_start: 0.6874 (t80) cc_final: 0.6592 (t80) REVERT: D 64 MET cc_start: 0.8884 (pmm) cc_final: 0.8495 (pmm) REVERT: D 92 MET cc_start: 0.8699 (mmt) cc_final: 0.8427 (mpp) REVERT: D 176 LEU cc_start: 0.8458 (OUTLIER) cc_final: 0.8216 (tt) REVERT: D 208 GLU cc_start: 0.8248 (pp20) cc_final: 0.7867 (tm-30) REVERT: D 218 MET cc_start: 0.9115 (tpt) cc_final: 0.8833 (tpp) REVERT: D 327 THR cc_start: 0.6440 (OUTLIER) cc_final: 0.5953 (t) REVERT: D 429 GLU cc_start: 0.8310 (OUTLIER) cc_final: 0.8037 (mp0) REVERT: D 449 MET cc_start: 0.9185 (ttt) cc_final: 0.8771 (ttt) REVERT: D 917 ASP cc_start: 0.8596 (OUTLIER) cc_final: 0.8364 (m-30) REVERT: E 27 MET cc_start: 0.7793 (tmm) cc_final: 0.7360 (tmm) REVERT: E 195 ASP cc_start: 0.9189 (OUTLIER) cc_final: 0.8720 (t0) REVERT: F 449 MET cc_start: 0.7937 (ttp) cc_final: 0.7693 (ttp) REVERT: F 775 ASP cc_start: 0.8404 (m-30) cc_final: 0.8129 (m-30) REVERT: F 868 THR cc_start: 0.9092 (OUTLIER) cc_final: 0.8845 (m) REVERT: G 30 GLU cc_start: 0.8795 (pp20) cc_final: 0.8412 (mp0) REVERT: G 46 GLU cc_start: 0.7847 (tp30) cc_final: 0.7302 (tt0) REVERT: G 54 LYS cc_start: 0.8292 (tttt) cc_final: 0.8070 (ttmt) REVERT: H 18 GLU cc_start: 0.8622 (tt0) cc_final: 0.8397 (tm-30) REVERT: I 17 GLU cc_start: 0.8544 (tp30) cc_final: 0.8239 (tp30) REVERT: I 18 GLU cc_start: 0.9326 (tt0) cc_final: 0.8993 (tp30) REVERT: I 44 MET cc_start: 0.7084 (OUTLIER) cc_final: 0.6770 (tmm) outliers start: 43 outliers final: 28 residues processed: 340 average time/residue: 0.1335 time to fit residues: 72.6810 Evaluate side-chains 334 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 299 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 54 GLU Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 187 THR Chi-restraints excluded: chain D residue 302 MET Chi-restraints excluded: chain D residue 327 THR Chi-restraints excluded: chain D residue 387 VAL Chi-restraints excluded: chain D residue 429 GLU Chi-restraints excluded: chain D residue 902 VAL Chi-restraints excluded: chain D residue 915 LEU Chi-restraints excluded: chain D residue 917 ASP Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain E residue 195 ASP Chi-restraints excluded: chain E residue 204 LEU Chi-restraints excluded: chain E residue 291 LEU Chi-restraints excluded: chain E residue 323 CYS Chi-restraints excluded: chain E residue 832 HIS Chi-restraints excluded: chain E residue 833 TRP Chi-restraints excluded: chain E residue 840 VAL Chi-restraints excluded: chain E residue 928 SER Chi-restraints excluded: chain F residue 406 LEU Chi-restraints excluded: chain F residue 833 TRP Chi-restraints excluded: chain F residue 835 VAL Chi-restraints excluded: chain F residue 867 ASN Chi-restraints excluded: chain F residue 868 THR Chi-restraints excluded: chain F residue 914 LEU Chi-restraints excluded: chain F residue 942 VAL Chi-restraints excluded: chain H residue 17 GLU Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain I residue 44 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 172 optimal weight: 7.9990 chunk 115 optimal weight: 0.3980 chunk 6 optimal weight: 10.0000 chunk 133 optimal weight: 1.9990 chunk 212 optimal weight: 2.9990 chunk 102 optimal weight: 0.9990 chunk 168 optimal weight: 6.9990 chunk 124 optimal weight: 2.9990 chunk 12 optimal weight: 0.2980 chunk 3 optimal weight: 10.0000 chunk 147 optimal weight: 0.0870 overall best weight: 0.7562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 26 GLN E 58 GLN ** E 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 729 GLN E 832 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.088279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.071978 restraints weight = 52721.838| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 3.52 r_work: 0.3020 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.2666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 19776 Z= 0.126 Angle : 0.621 12.894 26893 Z= 0.307 Chirality : 0.044 0.460 3227 Planarity : 0.004 0.038 3377 Dihedral : 8.256 159.666 2845 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.08 % Allowed : 20.85 % Favored : 77.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.09 (0.17), residues: 2516 helix: 2.07 (0.12), residues: 1691 sheet: 1.52 (0.44), residues: 150 loop : -0.38 (0.24), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 99 TYR 0.012 0.001 TYR D 223 PHE 0.017 0.001 PHE E 364 TRP 0.010 0.001 TRP E 379 HIS 0.003 0.001 HIS F 722 Details of bonding type rmsd covalent geometry : bond 0.00284 (19776) covalent geometry : angle 0.62104 (26893) hydrogen bonds : bond 0.04107 ( 1395) hydrogen bonds : angle 4.23309 ( 4143) ********************** 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 345 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 303 time to evaluate : 0.765 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 7 ARG cc_start: 0.8113 (mtp-110) cc_final: 0.7641 (mmp-170) REVERT: B 27 ARG cc_start: 0.8811 (tpp-160) cc_final: 0.7157 (ttt180) REVERT: D 64 MET cc_start: 0.8902 (pmm) cc_final: 0.8676 (pmm) REVERT: D 92 MET cc_start: 0.8685 (mmt) cc_final: 0.8410 (mpp) REVERT: D 176 LEU cc_start: 0.8467 (OUTLIER) cc_final: 0.8219 (tt) REVERT: D 208 GLU cc_start: 0.8231 (pp20) cc_final: 0.7815 (tm-30) REVERT: D 218 MET cc_start: 0.9082 (tpt) cc_final: 0.8791 (tpp) REVERT: D 327 THR cc_start: 0.6618 (OUTLIER) cc_final: 0.6095 (t) REVERT: D 429 GLU cc_start: 0.8310 (OUTLIER) cc_final: 0.8038 (mp0) REVERT: D 449 MET cc_start: 0.9183 (ttt) cc_final: 0.8772 (ttt) REVERT: D 917 ASP cc_start: 0.8668 (OUTLIER) cc_final: 0.8424 (m-30) REVERT: E 27 MET cc_start: 0.7827 (tmm) cc_final: 0.7387 (tmm) REVERT: E 195 ASP cc_start: 0.9195 (OUTLIER) cc_final: 0.8525 (t0) REVERT: E 443 MET cc_start: 0.8636 (mmp) cc_final: 0.7883 (mmp) REVERT: F 449 MET cc_start: 0.7964 (ttp) cc_final: 0.7705 (ttp) REVERT: F 775 ASP cc_start: 0.8386 (m-30) cc_final: 0.8110 (m-30) REVERT: F 868 THR cc_start: 0.9115 (OUTLIER) cc_final: 0.8866 (m) REVERT: G 17 GLU cc_start: 0.9047 (tt0) cc_final: 0.8731 (tt0) REVERT: G 18 GLU cc_start: 0.8624 (tm-30) cc_final: 0.8356 (tm-30) REVERT: G 23 GLU cc_start: 0.9032 (mm-30) cc_final: 0.8753 (mm-30) REVERT: G 36 ASP cc_start: 0.9408 (t0) cc_final: 0.8616 (p0) REVERT: G 44 MET cc_start: 0.8318 (mmm) cc_final: 0.8073 (mmm) REVERT: G 54 LYS cc_start: 0.8305 (tttt) cc_final: 0.8071 (ttmt) REVERT: H 18 GLU cc_start: 0.8594 (tt0) cc_final: 0.8384 (tm-30) REVERT: I 17 GLU cc_start: 0.8565 (tp30) cc_final: 0.8224 (tp30) REVERT: I 18 GLU cc_start: 0.9316 (tt0) cc_final: 0.8971 (tp30) REVERT: I 44 MET cc_start: 0.7167 (OUTLIER) cc_final: 0.6846 (tmm) outliers start: 42 outliers final: 30 residues processed: 325 average time/residue: 0.1356 time to fit residues: 70.5686 Evaluate side-chains 335 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 298 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain D residue 29 ARG Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 187 THR Chi-restraints excluded: chain D residue 302 MET Chi-restraints excluded: chain D residue 327 THR Chi-restraints excluded: chain D residue 387 VAL Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain D residue 429 GLU Chi-restraints excluded: chain D residue 902 VAL Chi-restraints excluded: chain D residue 915 LEU Chi-restraints excluded: chain D residue 917 ASP Chi-restraints excluded: chain E residue 58 GLN Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain E residue 195 ASP Chi-restraints excluded: chain E residue 204 LEU Chi-restraints excluded: chain E residue 291 LEU Chi-restraints excluded: chain E residue 323 CYS Chi-restraints excluded: chain E residue 833 TRP Chi-restraints excluded: chain E residue 840 VAL Chi-restraints excluded: chain E residue 928 SER Chi-restraints excluded: chain F residue 406 LEU Chi-restraints excluded: chain F residue 833 TRP Chi-restraints excluded: chain F residue 835 VAL Chi-restraints excluded: chain F residue 852 LEU Chi-restraints excluded: chain F residue 867 ASN Chi-restraints excluded: chain F residue 868 THR Chi-restraints excluded: chain F residue 914 LEU Chi-restraints excluded: chain F residue 942 VAL Chi-restraints excluded: chain H residue 17 GLU Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain I residue 44 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 165 optimal weight: 1.9990 chunk 204 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 248 optimal weight: 6.9990 chunk 152 optimal weight: 0.9980 chunk 161 optimal weight: 7.9990 chunk 192 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 113 optimal weight: 0.8980 chunk 211 optimal weight: 3.9990 chunk 179 optimal weight: 4.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 26 GLN ** E 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 729 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 832 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.088167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.071917 restraints weight = 52628.337| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 3.51 r_work: 0.3018 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.2663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.433 19776 Z= 0.251 Angle : 0.795 65.900 26893 Z= 0.439 Chirality : 0.045 0.486 3227 Planarity : 0.005 0.184 3377 Dihedral : 8.256 159.669 2845 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.98 % Allowed : 21.20 % Favored : 76.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.09 (0.17), residues: 2516 helix: 2.06 (0.12), residues: 1691 sheet: 1.51 (0.44), residues: 150 loop : -0.38 (0.24), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 99 TYR 0.011 0.001 TYR D 223 PHE 0.014 0.001 PHE E 364 TRP 0.010 0.001 TRP E 379 HIS 0.004 0.001 HIS F 722 Details of bonding type rmsd covalent geometry : bond 0.00543 (19776) covalent geometry : angle 0.79500 (26893) hydrogen bonds : bond 0.04122 ( 1395) hydrogen bonds : angle 4.23531 ( 4143) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4090.64 seconds wall clock time: 71 minutes 15.88 seconds (4275.88 seconds total)