Starting phenix.real_space_refine on Mon May 4 09:04:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9rfu_53941/05_2026/9rfu_53941.cif Found real_map, /net/cci-nas-00/data/ceres_data/9rfu_53941/05_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 { model { file = "/net/cci-nas-00/data/ceres_data/9rfu_53941/05_2026/9rfu_53941.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9rfu_53941/05_2026/9rfu_53941.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9rfu_53941/05_2026/9rfu_53941.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9rfu_53941/05_2026/9rfu_53941.map" } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/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 Unresolved non-hydrogen dihedrals: 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 Unresolved non-hydrogen dihedrals: 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 Unresolved non-hydrogen dihedrals: 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: 3.60, per 1000 atoms: 0.19 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: 1.64 Conformation dependent library (CDL) restraints added in 728.0 milliseconds 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4648 Finding SS restraints... Secondary structure from input PDB file: 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: 0.62 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: 3.29 Time building geometry restraints manager: 2.19 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 1.642 1.489 0.153 2.00e-02 2.50e+03 5.87e+01 bond pdb=" OG 4HH I 41 " pdb=" P 4HH I 41 " ideal model delta sigma weight residual 1.642 1.491 0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" OG 4HH G 41 " pdb=" P 4HH G 41 " ideal model delta sigma weight residual 1.642 1.501 0.141 2.00e-02 2.50e+03 4.97e+01 bond pdb=" CL3 4HH I 41 " pdb=" NN 4HH I 41 " ideal model delta sigma weight residual 1.335 1.448 -0.113 2.00e-02 2.50e+03 3.20e+01 bond pdb=" CL3 4HH G 41 " pdb=" NN 4HH G 41 " ideal model delta sigma weight residual 1.335 1.448 -0.113 2.00e-02 2.50e+03 3.20e+01 ... (remaining 19771 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.76: 26817 3.76 - 7.51: 66 7.51 - 11.27: 5 11.27 - 15.03: 1 15.03 - 18.78: 4 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 117.42 136.20 -18.78 3.00e+00 1.11e-01 3.92e+01 angle pdb=" OG 4HH I 41 " pdb=" P 4HH I 41 " pdb=" O3P 4HH I 41 " ideal model delta sigma weight residual 92.93 109.46 -16.53 3.00e+00 1.11e-01 3.04e+01 angle pdb=" OG 4HH H 41 " pdb=" P 4HH H 41 " pdb=" O3P 4HH H 41 " ideal model delta sigma weight residual 92.93 109.39 -16.46 3.00e+00 1.11e-01 3.01e+01 angle pdb=" OG 4HH G 41 " pdb=" P 4HH G 41 " pdb=" O3P 4HH G 41 " ideal model delta sigma weight residual 92.93 109.39 -16.46 3.00e+00 1.11e-01 3.01e+01 angle pdb=" CB 4HH I 41 " pdb=" OG 4HH I 41 " pdb=" P 4HH I 41 " ideal model delta sigma weight residual 117.42 129.38 -11.96 3.00e+00 1.11e-01 1.59e+01 ... (remaining 26888 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.47: 11250 28.47 - 56.93: 529 56.93 - 85.40: 59 85.40 - 113.87: 8 113.87 - 142.33: 3 Dihedral angle restraints: 11849 sinusoidal: 4610 harmonic: 7239 Sorted by residual: 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 dihedral pdb=" CA GLU I 62 " pdb=" C GLU I 62 " pdb=" N ASP I 63 " pdb=" CA ASP I 63 " ideal model delta harmonic sigma weight residual 180.00 158.91 21.09 0 5.00e+00 4.00e-02 1.78e+01 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 -175.20 -44.64 -130.56 1 3.00e+01 1.11e-03 1.76e+01 ... (remaining 11846 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 2480 0.049 - 0.099: 628 0.099 - 0.148: 114 0.148 - 0.197: 4 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=" CM 4HH I 41 " pdb=" CK 4HH I 41 " pdb=" CL3 4HH I 41 " pdb=" OM 4HH I 41 " both_signs ideal model delta sigma weight residual False 2.34 2.50 -0.16 2.00e-01 2.50e+01 6.17e-01 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 ... (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: 3.880 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: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 16.720 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.800 ------------------------------------------------------------------------------- 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 0.153 19776 Z= 0.231 Angle : 0.696 18.783 26893 Z= 0.352 Chirality : 0.044 0.247 3227 Planarity : 0.005 0.066 3377 Dihedral : 15.838 142.333 7201 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 0.00497 (19776) covalent geometry : angle 0.69552 (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 : 0.664 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: 0.1307 time to fit residues: 77.3439 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 : 0.523 ------------------------------------------------------------------------------- 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 ** 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.085916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.069407 restraints weight = 52691.424| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 3.50 r_work: 0.2975 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.1334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 19776 Z= 0.145 Angle : 0.622 10.032 26893 Z= 0.316 Chirality : 0.043 0.227 3227 Planarity : 0.005 0.040 3377 Dihedral : 10.245 146.905 2917 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.93 % Allowed : 10.35 % Favored : 87.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.35 (0.17), residues: 2516 helix: 1.56 (0.12), residues: 1691 sheet: 1.51 (0.45), residues: 132 loop : -0.87 (0.23), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 224 TYR 0.016 0.002 TYR E 331 PHE 0.019 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 0.00314 (19776) covalent geometry : angle 0.62157 (26893) hydrogen bonds : bond 0.05291 ( 1395) hydrogen bonds : angle 4.72172 ( 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 350 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 311 time to evaluate : 0.667 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 LYS cc_start: 0.7232 (mmtp) cc_final: 0.6929 (mmtt) REVERT: B 7 ARG cc_start: 0.8032 (mtp180) cc_final: 0.7599 (mmp-170) REVERT: B 15 LEU cc_start: 0.9416 (OUTLIER) cc_final: 0.9177 (mm) REVERT: B 27 ARG cc_start: 0.8763 (tpp-160) cc_final: 0.7046 (ttt180) REVERT: D 54 GLU cc_start: 0.7734 (pt0) cc_final: 0.7530 (mp0) REVERT: D 72 MET cc_start: 0.9057 (tpp) cc_final: 0.8809 (tpp) REVERT: D 92 MET cc_start: 0.8896 (mmt) cc_final: 0.8405 (mmt) REVERT: D 183 LYS cc_start: 0.7737 (ptpt) cc_final: 0.7337 (ptmt) REVERT: D 352 THR cc_start: 0.8126 (m) cc_final: 0.7702 (p) REVERT: D 777 MET cc_start: 0.8952 (OUTLIER) cc_final: 0.8686 (ptp) REVERT: E 425 LEU cc_start: 0.8946 (mp) cc_final: 0.8722 (tt) REVERT: F 775 ASP cc_start: 0.8400 (m-30) cc_final: 0.8198 (m-30) REVERT: F 874 MET cc_start: 0.8588 (mmm) cc_final: 0.8060 (mmt) REVERT: H 14 GLU cc_start: 0.8719 (mt-10) cc_final: 0.8385 (mp0) REVERT: H 30 GLU cc_start: 0.8741 (OUTLIER) cc_final: 0.8441 (pm20) REVERT: I 17 GLU cc_start: 0.8496 (tp30) cc_final: 0.8200 (tp30) REVERT: I 40 ASP cc_start: 0.7359 (t0) cc_final: 0.7087 (t0) REVERT: I 46 GLU cc_start: 0.7495 (mt-10) cc_final: 0.7153 (mt-10) outliers start: 39 outliers final: 18 residues processed: 330 average time/residue: 0.1306 time to fit residues: 67.2262 Evaluate side-chains 306 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 285 time to evaluate : 0.731 ------------------------------------------------------------------------------- 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 291 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: 5.9990 chunk 38 optimal weight: 2.9990 chunk 228 optimal weight: 5.9990 chunk 161 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 76 optimal weight: 0.8980 chunk 233 optimal weight: 0.0170 chunk 133 optimal weight: 0.6980 chunk 217 optimal weight: 0.9980 chunk 110 optimal weight: 1.9990 overall best weight: 0.9220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 832 HIS ** F 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.086090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.069839 restraints weight = 53045.059| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 3.46 r_work: 0.2983 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.1650 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= 0.135 Angle : 0.574 8.661 26893 Z= 0.291 Chirality : 0.042 0.173 3227 Planarity : 0.004 0.038 3377 Dihedral : 9.939 144.528 2917 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.58 % Allowed : 12.78 % Favored : 84.65 % 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: 1.65 (0.17), residues: 2516 helix: 1.77 (0.12), residues: 1688 sheet: 1.61 (0.45), residues: 135 loop : -0.70 (0.24), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 68 TYR 0.015 0.001 TYR D 690 PHE 0.014 0.001 PHE E 129 TRP 0.012 0.001 TRP F 833 HIS 0.003 0.001 HIS F 722 Details of bonding type rmsd covalent geometry : bond 0.00298 (19776) covalent geometry : angle 0.57388 (26893) hydrogen bonds : bond 0.04844 ( 1395) hydrogen bonds : angle 4.45077 ( 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 362 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 310 time to evaluate : 0.694 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 LYS cc_start: 0.7275 (mmtp) cc_final: 0.7008 (mmtt) REVERT: B 7 ARG cc_start: 0.7970 (mtp180) cc_final: 0.7561 (mmp-170) REVERT: B 27 ARG cc_start: 0.8746 (tpp-160) cc_final: 0.7090 (ttt180) REVERT: D 64 MET cc_start: 0.8818 (pmm) cc_final: 0.8481 (pmm) REVERT: D 92 MET cc_start: 0.8817 (mmt) cc_final: 0.8335 (mmt) REVERT: D 208 GLU cc_start: 0.8285 (tm-30) cc_final: 0.8072 (tm-30) REVERT: D 352 THR cc_start: 0.8073 (m) cc_final: 0.7616 (p) REVERT: D 449 MET cc_start: 0.8951 (ttt) cc_final: 0.8524 (ttt) REVERT: D 777 MET cc_start: 0.8944 (OUTLIER) cc_final: 0.8688 (ptp) REVERT: D 917 ASP cc_start: 0.8615 (OUTLIER) cc_final: 0.8308 (m-30) REVERT: E 27 MET cc_start: 0.7817 (tmm) cc_final: 0.7594 (tmm) REVERT: E 412 ARG cc_start: 0.8916 (mmm-85) cc_final: 0.8395 (mmp80) REVERT: F 357 ILE cc_start: 0.6817 (OUTLIER) cc_final: 0.6599 (pt) REVERT: F 775 ASP cc_start: 0.8420 (m-30) cc_final: 0.8219 (m-30) REVERT: F 791 MET cc_start: 0.9128 (tpp) cc_final: 0.8908 (mmm) REVERT: F 874 MET cc_start: 0.8602 (mmm) cc_final: 0.8147 (mmt) REVERT: F 888 PHE cc_start: 0.9126 (t80) cc_final: 0.8902 (t80) REVERT: G 54 LYS cc_start: 0.8531 (tttt) cc_final: 0.8320 (ttmt) REVERT: I 17 GLU cc_start: 0.8472 (tp30) cc_final: 0.7524 (tp30) REVERT: I 18 GLU cc_start: 0.9283 (tt0) cc_final: 0.8928 (tp30) REVERT: I 46 GLU cc_start: 0.7415 (mt-10) cc_final: 0.7036 (mt-10) outliers start: 52 outliers final: 26 residues processed: 337 average time/residue: 0.1332 time to fit residues: 70.7654 Evaluate side-chains 315 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 286 time to evaluate : 0.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 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 E residue 914 LEU 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 942 VAL Chi-restraints excluded: chain H residue 30 GLU Chi-restraints excluded: chain H residue 45 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 51 optimal weight: 3.9990 chunk 215 optimal weight: 0.2980 chunk 229 optimal weight: 3.9990 chunk 36 optimal weight: 0.9990 chunk 14 optimal weight: 0.0070 chunk 3 optimal weight: 10.0000 chunk 68 optimal weight: 4.9990 chunk 91 optimal weight: 0.9990 chunk 17 optimal weight: 9.9990 chunk 6 optimal weight: 10.0000 chunk 226 optimal weight: 3.9990 overall best weight: 1.2604 ------------------------------------------------------------------------------- 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 F 163 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.085508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.069290 restraints weight = 53161.438| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 3.47 r_work: 0.2974 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.1836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 19776 Z= 0.148 Angle : 0.584 13.125 26893 Z= 0.295 Chirality : 0.043 0.347 3227 Planarity : 0.004 0.041 3377 Dihedral : 9.805 140.926 2917 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.77 % Allowed : 14.76 % Favored : 82.47 % 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: 1.74 (0.17), residues: 2516 helix: 1.83 (0.12), residues: 1688 sheet: 1.87 (0.45), residues: 132 loop : -0.64 (0.24), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 68 TYR 0.010 0.001 TYR D 277 PHE 0.018 0.001 PHE D 23 TRP 0.011 0.001 TRP F 833 HIS 0.003 0.001 HIS F 722 Details of bonding type rmsd covalent geometry : bond 0.00334 (19776) covalent geometry : angle 0.58399 (26893) hydrogen bonds : bond 0.04788 ( 1395) hydrogen bonds : angle 4.38205 ( 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 354 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 298 time to evaluate : 0.638 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 LYS cc_start: 0.7349 (mmtp) cc_final: 0.7090 (mmtt) REVERT: B 7 ARG cc_start: 0.8033 (mtp180) cc_final: 0.7598 (mmp-170) REVERT: B 27 ARG cc_start: 0.8810 (tpp-160) cc_final: 0.7112 (ttt180) REVERT: D 64 MET cc_start: 0.8863 (pmm) cc_final: 0.8521 (pmm) REVERT: D 92 MET cc_start: 0.8787 (mmt) cc_final: 0.8455 (mpp) REVERT: D 208 GLU cc_start: 0.8341 (tm-30) cc_final: 0.8136 (tm-30) REVERT: D 352 THR cc_start: 0.8128 (m) cc_final: 0.7671 (p) REVERT: D 429 GLU cc_start: 0.8239 (OUTLIER) cc_final: 0.7947 (mp0) REVERT: D 449 MET cc_start: 0.9059 (ttt) cc_final: 0.8597 (ttt) REVERT: D 777 MET cc_start: 0.8971 (OUTLIER) cc_final: 0.8708 (ptp) REVERT: E 27 MET cc_start: 0.7870 (tmm) cc_final: 0.7591 (tmm) REVERT: E 195 ASP cc_start: 0.9085 (OUTLIER) cc_final: 0.8465 (t0) REVERT: F 357 ILE cc_start: 0.6886 (OUTLIER) cc_final: 0.6662 (pt) REVERT: F 775 ASP cc_start: 0.8411 (m-30) cc_final: 0.8211 (m-30) REVERT: F 874 MET cc_start: 0.8592 (mmm) cc_final: 0.8219 (mmt) REVERT: G 30 GLU cc_start: 0.8721 (pp20) cc_final: 0.8151 (mp0) REVERT: G 54 LYS cc_start: 0.8490 (tttt) cc_final: 0.8265 (ttmt) REVERT: I 17 GLU cc_start: 0.8504 (tp30) cc_final: 0.8256 (tp30) REVERT: I 18 GLU cc_start: 0.9267 (tt0) cc_final: 0.8944 (tp30) outliers start: 56 outliers final: 38 residues processed: 329 average time/residue: 0.1309 time to fit residues: 68.2353 Evaluate side-chains 320 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 278 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 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 291 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 914 LEU Chi-restraints excluded: chain F residue 120 THR 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 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 919 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 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: 0.9990 chunk 65 optimal weight: 0.2980 chunk 37 optimal weight: 2.9990 chunk 60 optimal weight: 0.9980 chunk 169 optimal weight: 0.6980 chunk 47 optimal weight: 6.9990 chunk 212 optimal weight: 1.9990 chunk 6 optimal weight: 10.0000 chunk 28 optimal weight: 0.6980 chunk 29 optimal weight: 2.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.086460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.070263 restraints weight = 52465.241| |-----------------------------------------------------------------------------| r_work (start): 0.3128 rms_B_bonded: 3.47 r_work: 0.2996 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.2044 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= 0.124 Angle : 0.564 9.621 26893 Z= 0.286 Chirality : 0.042 0.284 3227 Planarity : 0.004 0.041 3377 Dihedral : 9.603 137.547 2917 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.63 % Allowed : 16.00 % Favored : 81.38 % 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: 1.84 (0.17), residues: 2516 helix: 1.91 (0.12), residues: 1691 sheet: 1.95 (0.45), residues: 132 loop : -0.66 (0.24), residues: 693 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 0.013 0.001 PHE D 816 TRP 0.010 0.001 TRP F 833 HIS 0.003 0.001 HIS F 722 Details of bonding type rmsd covalent geometry : bond 0.00268 (19776) covalent geometry : angle 0.56426 (26893) hydrogen bonds : bond 0.04504 ( 1395) hydrogen bonds : angle 4.27597 ( 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 359 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 306 time to evaluate : 0.724 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 15 LEU cc_start: 0.9311 (OUTLIER) cc_final: 0.9091 (mm) REVERT: B 27 ARG cc_start: 0.8791 (tpp-160) cc_final: 0.7098 (ttt180) REVERT: D 23 PHE cc_start: 0.7287 (t80) cc_final: 0.7046 (t80) REVERT: D 64 MET cc_start: 0.8858 (pmm) cc_final: 0.8519 (pmm) REVERT: D 92 MET cc_start: 0.8746 (mmt) cc_final: 0.8440 (mpp) REVERT: D 429 GLU cc_start: 0.8210 (OUTLIER) cc_final: 0.7937 (mp0) REVERT: D 449 MET cc_start: 0.9113 (ttt) cc_final: 0.8679 (ttt) REVERT: D 777 MET cc_start: 0.8983 (OUTLIER) cc_final: 0.8739 (ptp) REVERT: D 917 ASP cc_start: 0.8679 (OUTLIER) cc_final: 0.8403 (m-30) REVERT: E 27 MET cc_start: 0.7871 (tmm) cc_final: 0.7234 (tmm) REVERT: E 195 ASP cc_start: 0.9152 (OUTLIER) cc_final: 0.8621 (t0) REVERT: E 405 LEU cc_start: 0.8844 (OUTLIER) cc_final: 0.8563 (mt) REVERT: E 412 ARG cc_start: 0.8936 (mmm-85) cc_final: 0.8411 (mmp80) REVERT: F 775 ASP cc_start: 0.8354 (m-30) cc_final: 0.8128 (m-30) REVERT: F 874 MET cc_start: 0.8572 (mmm) cc_final: 0.8266 (mmt) REVERT: G 30 GLU cc_start: 0.8763 (pp20) cc_final: 0.8194 (mp0) REVERT: G 54 LYS cc_start: 0.8402 (tttt) cc_final: 0.8174 (ttmt) REVERT: I 17 GLU cc_start: 0.8525 (tp30) cc_final: 0.8293 (tp30) REVERT: I 18 GLU cc_start: 0.9264 (tt0) cc_final: 0.8921 (tp30) REVERT: I 44 MET cc_start: 0.7259 (tmm) cc_final: 0.6889 (tmm) outliers start: 53 outliers final: 34 residues processed: 334 average time/residue: 0.1326 time to fit residues: 70.0328 Evaluate side-chains 322 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 282 time to evaluate : 0.742 ------------------------------------------------------------------------------- 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 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 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 291 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 832 HIS Chi-restraints excluded: chain E residue 894 SER Chi-restraints excluded: chain E residue 914 LEU 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 862 ILE Chi-restraints excluded: chain F residue 867 ASN Chi-restraints excluded: chain F residue 914 LEU 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 95 optimal weight: 4.9990 chunk 26 optimal weight: 3.9990 chunk 47 optimal weight: 6.9990 chunk 177 optimal weight: 0.7980 chunk 236 optimal weight: 0.9980 chunk 106 optimal weight: 0.0980 chunk 7 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 52 optimal weight: 5.9990 chunk 148 optimal weight: 5.9990 chunk 211 optimal weight: 4.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.085666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.069263 restraints weight = 52820.854| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 3.49 r_work: 0.2978 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.2140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 19776 Z= 0.142 Angle : 0.572 9.300 26893 Z= 0.291 Chirality : 0.043 0.286 3227 Planarity : 0.004 0.040 3377 Dihedral : 9.441 133.117 2917 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 3.07 % Allowed : 17.78 % Favored : 79.15 % 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: 1.93 (0.17), residues: 2516 helix: 1.96 (0.12), residues: 1685 sheet: 1.43 (0.44), residues: 150 loop : -0.46 (0.24), residues: 681 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 68 TYR 0.012 0.001 TYR D 223 PHE 0.013 0.001 PHE F 888 TRP 0.011 0.001 TRP D 39 HIS 0.003 0.001 HIS F 722 Details of bonding type rmsd covalent geometry : bond 0.00324 (19776) covalent geometry : angle 0.57161 (26893) hydrogen bonds : bond 0.04593 ( 1395) hydrogen bonds : angle 4.28164 ( 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: 62 poor density : 293 time to evaluate : 0.710 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 7 ARG cc_start: 0.8143 (mtp-110) cc_final: 0.7660 (mmp-170) REVERT: B 27 ARG cc_start: 0.8847 (tpp-160) cc_final: 0.7184 (ttt180) REVERT: D 92 MET cc_start: 0.8748 (mmt) cc_final: 0.8366 (mpp) REVERT: D 176 LEU cc_start: 0.8488 (OUTLIER) cc_final: 0.8252 (tt) REVERT: D 218 MET cc_start: 0.9185 (tpt) cc_final: 0.8881 (tpp) REVERT: D 327 THR cc_start: 0.6857 (OUTLIER) cc_final: 0.6242 (t) REVERT: D 429 GLU cc_start: 0.8238 (OUTLIER) cc_final: 0.7982 (mp0) REVERT: D 449 MET cc_start: 0.9136 (ttt) cc_final: 0.8720 (ttt) REVERT: D 777 MET cc_start: 0.8986 (OUTLIER) cc_final: 0.8748 (ptp) REVERT: E 27 MET cc_start: 0.7916 (tmm) cc_final: 0.7273 (tmm) REVERT: E 176 LEU cc_start: 0.6897 (OUTLIER) cc_final: 0.6498 (tt) REVERT: E 195 ASP cc_start: 0.9163 (OUTLIER) cc_final: 0.8673 (t0) REVERT: E 218 MET cc_start: 0.8715 (tpp) cc_final: 0.8414 (tpp) REVERT: E 405 LEU cc_start: 0.8828 (OUTLIER) cc_final: 0.8540 (mt) REVERT: F 366 LYS cc_start: 0.8139 (tmmt) cc_final: 0.7913 (tmtt) REVERT: F 449 MET cc_start: 0.8017 (ttp) cc_final: 0.7806 (ttp) REVERT: F 775 ASP cc_start: 0.8371 (m-30) cc_final: 0.8143 (m-30) REVERT: G 30 GLU cc_start: 0.8807 (pp20) cc_final: 0.8360 (mp0) REVERT: G 54 LYS cc_start: 0.8403 (tttt) cc_final: 0.8086 (ttmm) REVERT: H 14 GLU cc_start: 0.8865 (mt-10) cc_final: 0.8576 (mp0) REVERT: H 18 GLU cc_start: 0.8859 (tt0) cc_final: 0.8541 (tm-30) REVERT: I 17 GLU cc_start: 0.8561 (tp30) cc_final: 0.8287 (tp30) REVERT: I 18 GLU cc_start: 0.9273 (tt0) cc_final: 0.8961 (tp30) REVERT: I 44 MET cc_start: 0.7219 (tmm) cc_final: 0.6877 (tmm) outliers start: 62 outliers final: 37 residues processed: 327 average time/residue: 0.1303 time to fit residues: 67.8516 Evaluate side-chains 322 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 278 time to evaluate : 0.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain B residue 13 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 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 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 894 SER Chi-restraints excluded: chain E residue 914 LEU Chi-restraints excluded: chain E residue 928 SER Chi-restraints excluded: chain F residue 120 THR Chi-restraints excluded: chain F residue 271 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 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 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 42 LEU Chi-restraints excluded: chain I residue 58 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 128 optimal weight: 4.9990 chunk 8 optimal weight: 0.3980 chunk 31 optimal weight: 6.9990 chunk 200 optimal weight: 0.1980 chunk 188 optimal weight: 0.7980 chunk 248 optimal weight: 3.9990 chunk 100 optimal weight: 2.9990 chunk 233 optimal weight: 4.9990 chunk 238 optimal weight: 0.2980 chunk 67 optimal weight: 3.9990 chunk 158 optimal weight: 3.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 ** 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 = 0.3440 r_free = 0.3440 target = 0.086772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.070592 restraints weight = 52890.527| |-----------------------------------------------------------------------------| r_work (start): 0.3119 rms_B_bonded: 3.49 r_work: 0.2987 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.2265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 19776 Z= 0.131 Angle : 0.580 12.326 26893 Z= 0.291 Chirality : 0.043 0.342 3227 Planarity : 0.004 0.042 3377 Dihedral : 9.314 130.143 2917 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 3.02 % Allowed : 18.38 % Favored : 78.60 % 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: 1.97 (0.17), residues: 2516 helix: 1.96 (0.12), residues: 1706 sheet: 1.48 (0.45), residues: 147 loop : -0.44 (0.25), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 68 TYR 0.018 0.001 TYR D 690 PHE 0.021 0.001 PHE D 23 TRP 0.009 0.001 TRP F 833 HIS 0.003 0.001 HIS F 722 Details of bonding type rmsd covalent geometry : bond 0.00296 (19776) covalent geometry : angle 0.57964 (26893) hydrogen bonds : bond 0.04466 ( 1395) hydrogen bonds : angle 4.24788 ( 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 355 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 294 time to evaluate : 0.690 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 7 ARG cc_start: 0.8136 (mtp-110) cc_final: 0.7637 (mmp-170) REVERT: B 27 ARG cc_start: 0.8813 (tpp-160) cc_final: 0.7140 (ttt180) REVERT: D 64 MET cc_start: 0.8899 (pmm) cc_final: 0.8520 (pmm) REVERT: D 92 MET cc_start: 0.8739 (mmt) cc_final: 0.8375 (mpp) REVERT: D 176 LEU cc_start: 0.8502 (OUTLIER) cc_final: 0.8259 (tt) REVERT: D 208 GLU cc_start: 0.8086 (tm-30) cc_final: 0.7875 (tm-30) REVERT: D 218 MET cc_start: 0.9160 (tpt) cc_final: 0.8863 (tpp) REVERT: D 327 THR cc_start: 0.6689 (OUTLIER) cc_final: 0.6097 (t) REVERT: D 429 GLU cc_start: 0.8260 (OUTLIER) cc_final: 0.7983 (mp0) REVERT: D 449 MET cc_start: 0.9183 (ttt) cc_final: 0.8739 (ttt) REVERT: D 777 MET cc_start: 0.8960 (OUTLIER) cc_final: 0.8719 (ptp) REVERT: E 27 MET cc_start: 0.7840 (tmm) cc_final: 0.7204 (tmm) REVERT: E 176 LEU cc_start: 0.6908 (OUTLIER) cc_final: 0.6484 (tt) REVERT: E 195 ASP cc_start: 0.9164 (OUTLIER) cc_final: 0.8676 (t0) REVERT: E 405 LEU cc_start: 0.8849 (OUTLIER) cc_final: 0.8555 (mt) REVERT: E 412 ARG cc_start: 0.8975 (mmm-85) cc_final: 0.8435 (mmp80) REVERT: F 366 LYS cc_start: 0.8155 (tmmt) cc_final: 0.7915 (tmtt) REVERT: F 449 MET cc_start: 0.8065 (ttp) cc_final: 0.7781 (ttp) REVERT: F 775 ASP cc_start: 0.8437 (m-30) cc_final: 0.8199 (m-30) REVERT: G 30 GLU cc_start: 0.8857 (pp20) cc_final: 0.8362 (mp0) REVERT: G 54 LYS cc_start: 0.8315 (tttt) cc_final: 0.8095 (ttmt) REVERT: H 18 GLU cc_start: 0.8821 (tt0) cc_final: 0.8504 (tm-30) REVERT: I 7 GLU cc_start: 0.9034 (pm20) cc_final: 0.8822 (pm20) REVERT: I 17 GLU cc_start: 0.8549 (tp30) cc_final: 0.8262 (tp30) REVERT: I 18 GLU cc_start: 0.9310 (tt0) cc_final: 0.8981 (tp30) REVERT: I 44 MET cc_start: 0.7137 (tmm) cc_final: 0.6803 (tmm) outliers start: 61 outliers final: 45 residues processed: 328 average time/residue: 0.1259 time to fit residues: 66.3117 Evaluate side-chains 336 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 284 time to evaluate : 0.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 12 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 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 387 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 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 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 833 TRP Chi-restraints excluded: chain E residue 894 SER Chi-restraints excluded: chain E residue 914 LEU 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 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 919 LEU Chi-restraints excluded: chain F residue 942 VAL Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain G residue 61 ASP 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 222 optimal weight: 1.9990 chunk 195 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 171 optimal weight: 0.0870 chunk 88 optimal weight: 0.8980 chunk 91 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 96 optimal weight: 0.9990 chunk 148 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 12 optimal weight: 0.0070 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 286 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.087104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.070694 restraints weight = 52628.000| |-----------------------------------------------------------------------------| r_work (start): 0.3123 rms_B_bonded: 3.51 r_work: 0.2992 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.2354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 19776 Z= 0.126 Angle : 0.579 11.553 26893 Z= 0.292 Chirality : 0.043 0.351 3227 Planarity : 0.004 0.041 3377 Dihedral : 9.186 127.143 2917 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 3.17 % Allowed : 18.77 % Favored : 78.06 % 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: 2.01 (0.17), residues: 2516 helix: 1.99 (0.12), residues: 1709 sheet: 1.53 (0.45), residues: 147 loop : -0.45 (0.24), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 68 TYR 0.014 0.001 TYR D 223 PHE 0.015 0.001 PHE E 249 TRP 0.010 0.001 TRP E 379 HIS 0.003 0.001 HIS E 122 Details of bonding type rmsd covalent geometry : bond 0.00280 (19776) covalent geometry : angle 0.57921 (26893) hydrogen bonds : bond 0.04367 ( 1395) hydrogen bonds : angle 4.23217 ( 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 366 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 302 time to evaluate : 0.700 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 7 ARG cc_start: 0.8164 (mtp-110) cc_final: 0.7657 (mmp-170) REVERT: B 27 ARG cc_start: 0.8786 (tpp-160) cc_final: 0.7130 (ttt180) REVERT: D 23 PHE cc_start: 0.7039 (t80) cc_final: 0.6726 (t80) REVERT: D 64 MET cc_start: 0.8899 (pmm) cc_final: 0.8536 (pmm) REVERT: D 92 MET cc_start: 0.8725 (mmt) cc_final: 0.8406 (mpp) REVERT: D 176 LEU cc_start: 0.8496 (OUTLIER) cc_final: 0.8249 (tt) REVERT: D 218 MET cc_start: 0.9157 (tpt) cc_final: 0.8862 (tpp) REVERT: D 327 THR cc_start: 0.6649 (OUTLIER) cc_final: 0.6082 (t) REVERT: D 429 GLU cc_start: 0.8298 (OUTLIER) cc_final: 0.8029 (mp0) REVERT: D 449 MET cc_start: 0.9179 (ttt) cc_final: 0.8741 (ttt) REVERT: D 777 MET cc_start: 0.8921 (OUTLIER) cc_final: 0.8625 (ptp) REVERT: D 917 ASP cc_start: 0.8691 (OUTLIER) cc_final: 0.8430 (m-30) REVERT: E 27 MET cc_start: 0.7824 (tmm) cc_final: 0.7208 (tmm) REVERT: E 176 LEU cc_start: 0.6900 (OUTLIER) cc_final: 0.6472 (tt) REVERT: E 195 ASP cc_start: 0.9174 (OUTLIER) cc_final: 0.8459 (t0) REVERT: E 218 MET cc_start: 0.8645 (tpp) cc_final: 0.8325 (tpp) REVERT: E 405 LEU cc_start: 0.8801 (OUTLIER) cc_final: 0.8499 (mt) REVERT: E 412 ARG cc_start: 0.8975 (mmm-85) cc_final: 0.8449 (mmp80) REVERT: F 366 LYS cc_start: 0.8165 (tmmt) cc_final: 0.7930 (tmtt) REVERT: F 775 ASP cc_start: 0.8422 (m-30) cc_final: 0.8180 (m-30) REVERT: F 868 THR cc_start: 0.9131 (OUTLIER) cc_final: 0.8874 (m) REVERT: G 54 LYS cc_start: 0.8275 (tttt) cc_final: 0.8067 (ttmt) REVERT: H 14 GLU cc_start: 0.8868 (mt-10) cc_final: 0.8598 (mp0) REVERT: H 18 GLU cc_start: 0.8805 (tt0) cc_final: 0.8489 (tm-30) REVERT: I 17 GLU cc_start: 0.8556 (tp30) cc_final: 0.8251 (tp30) REVERT: I 18 GLU cc_start: 0.9302 (tt0) cc_final: 0.9002 (tp30) REVERT: I 44 MET cc_start: 0.7123 (tmm) cc_final: 0.6794 (tmm) outliers start: 64 outliers final: 40 residues processed: 336 average time/residue: 0.1258 time to fit residues: 67.4342 Evaluate side-chains 337 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 288 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 12 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 407 THR Chi-restraints excluded: chain D residue 429 GLU Chi-restraints excluded: chain D residue 492 ILE 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 323 CYS Chi-restraints excluded: chain E residue 405 LEU Chi-restraints excluded: chain E residue 833 TRP Chi-restraints excluded: chain E residue 894 SER Chi-restraints excluded: chain E residue 914 LEU Chi-restraints excluded: chain E residue 928 SER Chi-restraints excluded: chain F residue 120 THR Chi-restraints excluded: chain F residue 271 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 868 THR Chi-restraints excluded: chain F residue 914 LEU Chi-restraints excluded: chain F residue 919 LEU Chi-restraints excluded: chain F residue 942 VAL Chi-restraints excluded: chain G residue 34 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 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: 0.9980 chunk 125 optimal weight: 0.9990 chunk 144 optimal weight: 0.8980 chunk 85 optimal weight: 0.9990 chunk 95 optimal weight: 0.8980 chunk 40 optimal weight: 0.0040 chunk 200 optimal weight: 0.9990 chunk 218 optimal weight: 0.9990 chunk 82 optimal weight: 0.0770 chunk 133 optimal weight: 3.9990 chunk 43 optimal weight: 0.7980 overall best weight: 0.5350 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 286 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.088085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.071760 restraints weight = 52281.912| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 3.50 r_work: 0.3015 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.2512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 19776 Z= 0.120 Angle : 0.592 12.216 26893 Z= 0.296 Chirality : 0.043 0.360 3227 Planarity : 0.004 0.042 3377 Dihedral : 9.005 124.791 2917 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.67 % Allowed : 19.42 % Favored : 77.91 % 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: 2.11 (0.17), residues: 2516 helix: 2.10 (0.12), residues: 1694 sheet: 1.47 (0.44), residues: 147 loop : -0.41 (0.24), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 68 TYR 0.020 0.001 TYR D 690 PHE 0.013 0.001 PHE D 888 TRP 0.011 0.001 TRP E 379 HIS 0.006 0.001 HIS F 722 Details of bonding type rmsd covalent geometry : bond 0.00259 (19776) covalent geometry : angle 0.59192 (26893) hydrogen bonds : bond 0.04191 ( 1395) hydrogen bonds : angle 4.21152 ( 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 355 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 301 time to evaluate : 0.621 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 7 ARG cc_start: 0.8133 (mtp-110) cc_final: 0.7638 (mmp-170) REVERT: B 27 ARG cc_start: 0.8800 (tpp-160) cc_final: 0.7146 (ttt180) REVERT: D 64 MET cc_start: 0.8900 (pmm) cc_final: 0.8537 (pmm) REVERT: D 72 MET cc_start: 0.9148 (tpp) cc_final: 0.8876 (tpp) REVERT: D 92 MET cc_start: 0.8706 (mmt) cc_final: 0.8413 (mpp) REVERT: D 176 LEU cc_start: 0.8478 (OUTLIER) cc_final: 0.8232 (tt) REVERT: D 218 MET cc_start: 0.9141 (tpt) cc_final: 0.8849 (tpp) REVERT: D 327 THR cc_start: 0.6489 (OUTLIER) cc_final: 0.5932 (t) REVERT: D 429 GLU cc_start: 0.8285 (OUTLIER) cc_final: 0.8021 (mp0) REVERT: D 449 MET cc_start: 0.9209 (ttt) cc_final: 0.8789 (ttt) REVERT: D 777 MET cc_start: 0.8825 (ptm) cc_final: 0.8490 (ptp) REVERT: D 917 ASP cc_start: 0.8667 (OUTLIER) cc_final: 0.8430 (m-30) REVERT: E 27 MET cc_start: 0.7818 (tmm) cc_final: 0.7219 (tmm) REVERT: E 195 ASP cc_start: 0.9172 (OUTLIER) cc_final: 0.8562 (t0) REVERT: E 443 MET cc_start: 0.8648 (mmp) cc_final: 0.7961 (mmp) REVERT: F 366 LYS cc_start: 0.8196 (tmmt) cc_final: 0.7965 (tmtt) REVERT: F 775 ASP cc_start: 0.8405 (m-30) cc_final: 0.8152 (m-30) REVERT: F 868 THR cc_start: 0.9112 (OUTLIER) cc_final: 0.8862 (m) REVERT: G 54 LYS cc_start: 0.8278 (tttt) cc_final: 0.8070 (ttmt) REVERT: H 14 GLU cc_start: 0.8813 (mt-10) cc_final: 0.8502 (mp0) REVERT: H 18 GLU cc_start: 0.8724 (tt0) cc_final: 0.8453 (tm-30) REVERT: I 17 GLU cc_start: 0.8557 (tp30) cc_final: 0.8246 (tp30) REVERT: I 18 GLU cc_start: 0.9327 (tt0) cc_final: 0.9009 (tp30) REVERT: I 44 MET cc_start: 0.7077 (tmm) cc_final: 0.6744 (tmm) outliers start: 54 outliers final: 37 residues processed: 334 average time/residue: 0.1252 time to fit residues: 66.4845 Evaluate side-chains 332 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 289 time to evaluate : 0.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 12 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 24 ILE Chi-restraints excluded: chain D residue 29 ARG 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 492 ILE 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 832 HIS Chi-restraints excluded: chain E residue 833 TRP Chi-restraints excluded: chain E residue 894 SER Chi-restraints excluded: chain E residue 914 LEU 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 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 919 LEU Chi-restraints excluded: chain F residue 942 VAL Chi-restraints excluded: chain G residue 34 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 172 optimal weight: 2.9990 chunk 115 optimal weight: 0.7980 chunk 6 optimal weight: 10.0000 chunk 133 optimal weight: 0.2980 chunk 212 optimal weight: 2.9990 chunk 102 optimal weight: 0.9990 chunk 168 optimal weight: 0.0770 chunk 124 optimal weight: 0.0010 chunk 12 optimal weight: 0.9980 chunk 3 optimal weight: 10.0000 chunk 147 optimal weight: 1.9990 overall best weight: 0.4344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 286 GLN E 729 GLN H 78 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.088611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.072313 restraints weight = 52224.459| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 3.51 r_work: 0.3028 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.2653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 19776 Z= 0.119 Angle : 0.604 14.074 26893 Z= 0.299 Chirality : 0.043 0.430 3227 Planarity : 0.004 0.043 3377 Dihedral : 8.821 123.162 2917 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.28 % Allowed : 20.26 % Favored : 77.46 % 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: 2.16 (0.17), residues: 2516 helix: 2.13 (0.12), residues: 1694 sheet: 1.53 (0.45), residues: 147 loop : -0.39 (0.24), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 857 TYR 0.012 0.001 TYR D 223 PHE 0.025 0.001 PHE D 23 TRP 0.011 0.001 TRP E 379 HIS 0.003 0.001 HIS F 722 Details of bonding type rmsd covalent geometry : bond 0.00255 (19776) covalent geometry : angle 0.60360 (26893) hydrogen bonds : bond 0.04030 ( 1395) hydrogen bonds : angle 4.20405 ( 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 344 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 298 time to evaluate : 0.771 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: 0.7646 (mmp-170) REVERT: B 27 ARG cc_start: 0.8791 (tpp-160) cc_final: 0.7142 (ttt180) REVERT: D 64 MET cc_start: 0.8906 (pmm) cc_final: 0.8676 (pmm) REVERT: D 92 MET cc_start: 0.8717 (mmt) cc_final: 0.8461 (mpp) REVERT: D 176 LEU cc_start: 0.8468 (OUTLIER) cc_final: 0.8221 (tt) REVERT: D 218 MET cc_start: 0.9105 (tpt) cc_final: 0.8806 (tpp) REVERT: D 327 THR cc_start: 0.6482 (OUTLIER) cc_final: 0.5913 (t) REVERT: D 429 GLU cc_start: 0.8325 (OUTLIER) cc_final: 0.8044 (mp0) REVERT: D 449 MET cc_start: 0.9205 (ttt) cc_final: 0.8789 (ttt) REVERT: D 917 ASP cc_start: 0.8648 (OUTLIER) cc_final: 0.8401 (m-30) REVERT: E 27 MET cc_start: 0.7814 (tmm) cc_final: 0.7384 (tmm) REVERT: E 195 ASP cc_start: 0.9174 (OUTLIER) cc_final: 0.8597 (t0) REVERT: E 412 ARG cc_start: 0.8874 (tpp-160) cc_final: 0.8609 (tpp80) REVERT: F 366 LYS cc_start: 0.8193 (tmmt) cc_final: 0.7979 (tmtt) REVERT: F 775 ASP cc_start: 0.8406 (m-30) cc_final: 0.8129 (m-30) REVERT: F 868 THR cc_start: 0.9105 (OUTLIER) cc_final: 0.8856 (m) REVERT: G 54 LYS cc_start: 0.8257 (tttt) cc_final: 0.8029 (ttmt) REVERT: H 14 GLU cc_start: 0.8809 (mt-10) cc_final: 0.8506 (mp0) REVERT: H 18 GLU cc_start: 0.8660 (tt0) cc_final: 0.8437 (tm-30) REVERT: I 17 GLU cc_start: 0.8569 (tp30) cc_final: 0.8236 (tp30) REVERT: I 18 GLU cc_start: 0.9319 (tt0) cc_final: 0.8956 (tp30) REVERT: I 44 MET cc_start: 0.7060 (tmm) cc_final: 0.6734 (tmm) outliers start: 46 outliers final: 36 residues processed: 326 average time/residue: 0.1252 time to fit residues: 65.6811 Evaluate side-chains 333 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 291 time to evaluate : 0.730 ------------------------------------------------------------------------------- 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 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 492 ILE 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 729 GLN Chi-restraints excluded: chain E residue 832 HIS Chi-restraints excluded: chain E residue 833 TRP Chi-restraints excluded: chain E residue 894 SER Chi-restraints excluded: chain E residue 914 LEU 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 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 919 LEU Chi-restraints excluded: chain F residue 942 VAL Chi-restraints excluded: chain G residue 34 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 H residue 78 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 165 optimal weight: 0.4980 chunk 204 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 248 optimal weight: 0.7980 chunk 152 optimal weight: 0.8980 chunk 161 optimal weight: 6.9990 chunk 192 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 chunk 113 optimal weight: 0.5980 chunk 211 optimal weight: 0.8980 chunk 179 optimal weight: 4.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 286 GLN E 729 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.088383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.072298 restraints weight = 52171.274| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 3.49 r_work: 0.3027 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.2657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.180 19776 Z= 0.203 Angle : 0.902 59.199 26893 Z= 0.514 Chirality : 0.045 0.441 3227 Planarity : 0.004 0.043 3377 Dihedral : 8.834 123.167 2917 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.18 % Allowed : 20.60 % Favored : 77.22 % Cbeta Deviations : 0.04 % 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: 2.13 (0.17), residues: 2516 helix: 2.10 (0.12), residues: 1694 sheet: 1.53 (0.45), residues: 147 loop : -0.38 (0.24), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 68 TYR 0.012 0.001 TYR D 223 PHE 0.015 0.001 PHE D 23 TRP 0.010 0.001 TRP E 379 HIS 0.004 0.000 HIS F 722 Details of bonding type rmsd covalent geometry : bond 0.00409 (19776) covalent geometry : angle 0.90199 (26893) hydrogen bonds : bond 0.04060 ( 1395) hydrogen bonds : angle 4.21249 ( 4143) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3622.39 seconds wall clock time: 63 minutes 7.52 seconds (3787.52 seconds total)