Starting phenix.real_space_refine on Thu Mar 5 00:48:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7d5k_30583/03_2026/7d5k_30583.cif Found real_map, /net/cci-nas-00/data/ceres_data/7d5k_30583/03_2026/7d5k_30583.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7d5k_30583/03_2026/7d5k_30583.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7d5k_30583/03_2026/7d5k_30583.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7d5k_30583/03_2026/7d5k_30583.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7d5k_30583/03_2026/7d5k_30583.map" } resolution = 3.5 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= 0.052 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: 4 Type Number sf(0) Gaussians S 102 5.16 5 C 11559 2.51 5 N 2928 2.21 5 O 3078 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 48 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17667 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 5843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 727, 5843 Classifications: {'peptide': 727} Link IDs: {'PTRANS': 47, 'TRANS': 679} Chain breaks: 2 Chain: "B" Number of atoms: 5843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 727, 5843 Classifications: {'peptide': 727} Link IDs: {'PTRANS': 47, 'TRANS': 679} Chain breaks: 2 Chain: "C" Number of atoms: 5843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 727, 5843 Classifications: {'peptide': 727} Link IDs: {'PTRANS': 47, 'TRANS': 679} Chain breaks: 2 Chain: "D" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 23 Unusual residues: {'BGC': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 23 Unusual residues: {'BGC': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 23 Unusual residues: {'BGC': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 23 Unusual residues: {'BGC': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "H" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 23 Unusual residues: {'BGC': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "I" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 23 Unusual residues: {'BGC': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 4.31, per 1000 atoms: 0.24 Number of scatterers: 17667 At special positions: 0 Unit cell: (136.962, 138.049, 109.787, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 102 16.00 O 3078 8.00 N 2928 7.00 C 11559 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 Links applied BETA1-4 " BGC D 1 " - " BGC D 2 " " BGC E 1 " - " BGC E 2 " " BGC F 1 " - " BGC F 2 " " BGC G 1 " - " BGC G 2 " " BGC H 1 " - " BGC H 2 " " BGC I 1 " - " BGC I 2 " Time building additional restraints: 1.57 Conformation dependent library (CDL) restraints added in 970.2 milliseconds 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4068 Finding SS restraints... Secondary structure from input PDB file: 87 helices and 9 sheets defined 57.1% alpha, 6.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.58 Creating SS restraints... Processing helix chain 'A' and resid 246 through 249 Processing helix chain 'A' and resid 250 through 274 Processing helix chain 'A' and resid 279 through 302 removed outlier: 4.149A pdb=" N TRP A 283 " --> pdb=" O ALA A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 305 No H-bonds generated for 'chain 'A' and resid 303 through 305' Processing helix chain 'A' and resid 313 through 322 removed outlier: 3.649A pdb=" N LEU A 317 " --> pdb=" O TYR A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 359 removed outlier: 3.516A pdb=" N THR A 350 " --> pdb=" O PRO A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 366 Processing helix chain 'A' and resid 377 through 402 removed outlier: 3.904A pdb=" N PHE A 381 " --> pdb=" O SER A 377 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N ARG A 392 " --> pdb=" O ALA A 388 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N LYS A 393 " --> pdb=" O GLU A 389 " (cutoff:3.500A) Proline residue: A 396 - end of helix Processing helix chain 'A' and resid 407 through 412 Processing helix chain 'A' and resid 426 through 453 removed outlier: 4.086A pdb=" N ARG A 436 " --> pdb=" O ARG A 432 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLU A 437 " --> pdb=" O ALA A 433 " (cutoff:3.500A) Processing helix chain 'A' and resid 516 through 531 removed outlier: 3.839A pdb=" N VAL A 529 " --> pdb=" O ARG A 525 " (cutoff:3.500A) Processing helix chain 'A' and resid 549 through 559 removed outlier: 3.906A pdb=" N CYS A 556 " --> pdb=" O ARG A 552 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N PHE A 557 " --> pdb=" O GLU A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 589 through 595 removed outlier: 3.589A pdb=" N PHE A 593 " --> pdb=" O ASN A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 595 through 601 Processing helix chain 'A' and resid 617 through 621 removed outlier: 3.580A pdb=" N TYR A 621 " --> pdb=" O ARG A 617 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 617 through 621' Processing helix chain 'A' and resid 676 through 684 removed outlier: 3.881A pdb=" N PHE A 680 " --> pdb=" O SER A 676 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 695 Processing helix chain 'A' and resid 706 through 718 removed outlier: 3.699A pdb=" N LEU A 710 " --> pdb=" O SER A 706 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N ILE A 715 " --> pdb=" O LEU A 711 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N HIS A 716 " --> pdb=" O LYS A 712 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ILE A 718 " --> pdb=" O ALA A 714 " (cutoff:3.500A) Processing helix chain 'A' and resid 741 through 751 removed outlier: 3.811A pdb=" N MET A 749 " --> pdb=" O THR A 745 " (cutoff:3.500A) Processing helix chain 'A' and resid 773 through 792 Processing helix chain 'A' and resid 809 through 822 Processing helix chain 'A' and resid 825 through 841 removed outlier: 3.560A pdb=" N LEU A 830 " --> pdb=" O SER A 826 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ALA A 831 " --> pdb=" O LEU A 827 " (cutoff:3.500A) Proline residue: A 836 - end of helix Processing helix chain 'A' and resid 853 through 877 removed outlier: 4.218A pdb=" N PHE A 857 " --> pdb=" O PHE A 853 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N PHE A 862 " --> pdb=" O PHE A 858 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N TRP A 875 " --> pdb=" O LEU A 871 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLY A 877 " --> pdb=" O LEU A 873 " (cutoff:3.500A) Processing helix chain 'A' and resid 879 through 895 removed outlier: 4.149A pdb=" N VAL A 891 " --> pdb=" O GLU A 887 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 912 Processing helix chain 'A' and resid 938 through 940 No H-bonds generated for 'chain 'A' and resid 938 through 940' Processing helix chain 'A' and resid 941 through 965 removed outlier: 3.590A pdb=" N THR A 945 " --> pdb=" O LEU A 941 " (cutoff:3.500A) Processing helix chain 'A' and resid 972 through 996 removed outlier: 4.195A pdb=" N LYS A 976 " --> pdb=" O PRO A 972 " (cutoff:3.500A) Proline residue: A 989 - end of helix Processing helix chain 'A' and resid 1004 through 1024 Processing helix chain 'B' and resid 246 through 249 Processing helix chain 'B' and resid 250 through 274 Processing helix chain 'B' and resid 279 through 302 removed outlier: 4.148A pdb=" N TRP B 283 " --> pdb=" O ALA B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 303 through 305 No H-bonds generated for 'chain 'B' and resid 303 through 305' Processing helix chain 'B' and resid 313 through 322 removed outlier: 3.649A pdb=" N LEU B 317 " --> pdb=" O TYR B 313 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 359 removed outlier: 3.517A pdb=" N THR B 350 " --> pdb=" O PRO B 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 363 through 366 Processing helix chain 'B' and resid 377 through 402 removed outlier: 3.904A pdb=" N PHE B 381 " --> pdb=" O SER B 377 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N ARG B 392 " --> pdb=" O ALA B 388 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N LYS B 393 " --> pdb=" O GLU B 389 " (cutoff:3.500A) Proline residue: B 396 - end of helix Processing helix chain 'B' and resid 407 through 412 Processing helix chain 'B' and resid 426 through 453 removed outlier: 4.086A pdb=" N ARG B 436 " --> pdb=" O ARG B 432 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLU B 437 " --> pdb=" O ALA B 433 " (cutoff:3.500A) Processing helix chain 'B' and resid 516 through 531 removed outlier: 3.840A pdb=" N VAL B 529 " --> pdb=" O ARG B 525 " (cutoff:3.500A) Processing helix chain 'B' and resid 549 through 559 removed outlier: 3.906A pdb=" N CYS B 556 " --> pdb=" O ARG B 552 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N PHE B 557 " --> pdb=" O GLU B 553 " (cutoff:3.500A) Processing helix chain 'B' and resid 589 through 595 removed outlier: 3.590A pdb=" N PHE B 593 " --> pdb=" O ASN B 589 " (cutoff:3.500A) Processing helix chain 'B' and resid 595 through 601 Processing helix chain 'B' and resid 617 through 621 removed outlier: 3.580A pdb=" N TYR B 621 " --> pdb=" O ARG B 617 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 617 through 621' Processing helix chain 'B' and resid 676 through 684 removed outlier: 3.881A pdb=" N PHE B 680 " --> pdb=" O SER B 676 " (cutoff:3.500A) Processing helix chain 'B' and resid 687 through 695 Processing helix chain 'B' and resid 706 through 718 removed outlier: 3.698A pdb=" N LEU B 710 " --> pdb=" O SER B 706 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N ILE B 715 " --> pdb=" O LEU B 711 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N HIS B 716 " --> pdb=" O LYS B 712 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ILE B 718 " --> pdb=" O ALA B 714 " (cutoff:3.500A) Processing helix chain 'B' and resid 741 through 751 removed outlier: 3.811A pdb=" N MET B 749 " --> pdb=" O THR B 745 " (cutoff:3.500A) Processing helix chain 'B' and resid 773 through 792 Processing helix chain 'B' and resid 809 through 822 Processing helix chain 'B' and resid 825 through 841 removed outlier: 3.561A pdb=" N LEU B 830 " --> pdb=" O SER B 826 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ALA B 831 " --> pdb=" O LEU B 827 " (cutoff:3.500A) Proline residue: B 836 - end of helix Processing helix chain 'B' and resid 853 through 877 removed outlier: 4.218A pdb=" N PHE B 857 " --> pdb=" O PHE B 853 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N PHE B 862 " --> pdb=" O PHE B 858 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N TRP B 875 " --> pdb=" O LEU B 871 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLY B 877 " --> pdb=" O LEU B 873 " (cutoff:3.500A) Processing helix chain 'B' and resid 879 through 895 removed outlier: 4.150A pdb=" N VAL B 891 " --> pdb=" O GLU B 887 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 912 Processing helix chain 'B' and resid 938 through 940 No H-bonds generated for 'chain 'B' and resid 938 through 940' Processing helix chain 'B' and resid 941 through 965 removed outlier: 3.590A pdb=" N THR B 945 " --> pdb=" O LEU B 941 " (cutoff:3.500A) Processing helix chain 'B' and resid 972 through 996 removed outlier: 4.194A pdb=" N LYS B 976 " --> pdb=" O PRO B 972 " (cutoff:3.500A) Proline residue: B 989 - end of helix Processing helix chain 'B' and resid 1004 through 1024 Processing helix chain 'C' and resid 246 through 249 Processing helix chain 'C' and resid 250 through 274 Processing helix chain 'C' and resid 279 through 302 removed outlier: 4.148A pdb=" N TRP C 283 " --> pdb=" O ALA C 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 303 through 305 No H-bonds generated for 'chain 'C' and resid 303 through 305' Processing helix chain 'C' and resid 313 through 322 removed outlier: 3.648A pdb=" N LEU C 317 " --> pdb=" O TYR C 313 " (cutoff:3.500A) Processing helix chain 'C' and resid 346 through 359 removed outlier: 3.516A pdb=" N THR C 350 " --> pdb=" O PRO C 346 " (cutoff:3.500A) Processing helix chain 'C' and resid 363 through 366 Processing helix chain 'C' and resid 377 through 402 removed outlier: 3.905A pdb=" N PHE C 381 " --> pdb=" O SER C 377 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N GLU C 389 " --> pdb=" O SER C 385 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N ARG C 392 " --> pdb=" O ALA C 388 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N LYS C 393 " --> pdb=" O GLU C 389 " (cutoff:3.500A) Proline residue: C 396 - end of helix Processing helix chain 'C' and resid 407 through 412 Processing helix chain 'C' and resid 426 through 453 removed outlier: 4.086A pdb=" N ARG C 436 " --> pdb=" O ARG C 432 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLU C 437 " --> pdb=" O ALA C 433 " (cutoff:3.500A) Processing helix chain 'C' and resid 516 through 531 removed outlier: 3.840A pdb=" N VAL C 529 " --> pdb=" O ARG C 525 " (cutoff:3.500A) Processing helix chain 'C' and resid 549 through 559 removed outlier: 3.907A pdb=" N CYS C 556 " --> pdb=" O ARG C 552 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N PHE C 557 " --> pdb=" O GLU C 553 " (cutoff:3.500A) Processing helix chain 'C' and resid 589 through 595 removed outlier: 3.591A pdb=" N PHE C 593 " --> pdb=" O ASN C 589 " (cutoff:3.500A) Processing helix chain 'C' and resid 595 through 601 Processing helix chain 'C' and resid 617 through 621 removed outlier: 3.580A pdb=" N TYR C 621 " --> pdb=" O ARG C 617 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 617 through 621' Processing helix chain 'C' and resid 676 through 684 removed outlier: 3.880A pdb=" N PHE C 680 " --> pdb=" O SER C 676 " (cutoff:3.500A) Processing helix chain 'C' and resid 687 through 695 Processing helix chain 'C' and resid 706 through 718 removed outlier: 3.698A pdb=" N LEU C 710 " --> pdb=" O SER C 706 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N ILE C 715 " --> pdb=" O LEU C 711 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N HIS C 716 " --> pdb=" O LYS C 712 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ILE C 718 " --> pdb=" O ALA C 714 " (cutoff:3.500A) Processing helix chain 'C' and resid 741 through 751 removed outlier: 3.812A pdb=" N MET C 749 " --> pdb=" O THR C 745 " (cutoff:3.500A) Processing helix chain 'C' and resid 773 through 792 Processing helix chain 'C' and resid 809 through 822 Processing helix chain 'C' and resid 825 through 841 removed outlier: 3.560A pdb=" N LEU C 830 " --> pdb=" O SER C 826 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ALA C 831 " --> pdb=" O LEU C 827 " (cutoff:3.500A) Proline residue: C 836 - end of helix Processing helix chain 'C' and resid 853 through 877 removed outlier: 4.217A pdb=" N PHE C 857 " --> pdb=" O PHE C 853 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N PHE C 862 " --> pdb=" O PHE C 858 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N TRP C 875 " --> pdb=" O LEU C 871 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLY C 877 " --> pdb=" O LEU C 873 " (cutoff:3.500A) Processing helix chain 'C' and resid 879 through 895 removed outlier: 4.149A pdb=" N VAL C 891 " --> pdb=" O GLU C 887 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 912 Processing helix chain 'C' and resid 938 through 940 No H-bonds generated for 'chain 'C' and resid 938 through 940' Processing helix chain 'C' and resid 941 through 965 removed outlier: 3.590A pdb=" N THR C 945 " --> pdb=" O LEU C 941 " (cutoff:3.500A) Processing helix chain 'C' and resid 972 through 996 removed outlier: 4.194A pdb=" N LYS C 976 " --> pdb=" O PRO C 972 " (cutoff:3.500A) Proline residue: C 989 - end of helix Processing helix chain 'C' and resid 1004 through 1024 Processing sheet with id=AA1, first strand: chain 'A' and resid 240 through 244 Processing sheet with id=AA2, first strand: chain 'A' and resid 479 through 483 removed outlier: 6.160A pdb=" N CYS A 369 " --> pdb=" O VAL A 501 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N VAL A 503 " --> pdb=" O CYS A 369 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N ILE A 371 " --> pdb=" O VAL A 503 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N VAL A 333 " --> pdb=" O SER A 368 " (cutoff:3.500A) removed outlier: 8.202A pdb=" N TYR A 370 " --> pdb=" O VAL A 333 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N ILE A 335 " --> pdb=" O TYR A 370 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N SER A 372 " --> pdb=" O ILE A 335 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N VAL A 337 " --> pdb=" O SER A 372 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N ASP A 334 " --> pdb=" O LEU A 537 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N LEU A 539 " --> pdb=" O ASP A 334 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N PHE A 336 " --> pdb=" O LEU A 539 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N CYS A 613 " --> pdb=" O ASN A 538 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N CYS A 568 " --> pdb=" O ARG A 616 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N ILE A 757 " --> pdb=" O CYS A 568 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N VAL A 570 " --> pdb=" O ILE A 757 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 543 through 545 removed outlier: 6.524A pdb=" N ARG A 575 " --> pdb=" O GLY A 768 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 240 through 244 Processing sheet with id=AA5, first strand: chain 'B' and resid 479 through 483 removed outlier: 6.160A pdb=" N CYS B 369 " --> pdb=" O VAL B 501 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N VAL B 503 " --> pdb=" O CYS B 369 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N ILE B 371 " --> pdb=" O VAL B 503 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N VAL B 333 " --> pdb=" O SER B 368 " (cutoff:3.500A) removed outlier: 8.202A pdb=" N TYR B 370 " --> pdb=" O VAL B 333 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N ILE B 335 " --> pdb=" O TYR B 370 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N SER B 372 " --> pdb=" O ILE B 335 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N VAL B 337 " --> pdb=" O SER B 372 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N ASP B 334 " --> pdb=" O LEU B 537 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N LEU B 539 " --> pdb=" O ASP B 334 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N PHE B 336 " --> pdb=" O LEU B 539 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N CYS B 613 " --> pdb=" O ASN B 538 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N CYS B 568 " --> pdb=" O ARG B 616 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N ILE B 757 " --> pdb=" O CYS B 568 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N VAL B 570 " --> pdb=" O ILE B 757 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 543 through 545 removed outlier: 6.524A pdb=" N ARG B 575 " --> pdb=" O GLY B 768 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 240 through 244 Processing sheet with id=AA8, first strand: chain 'C' and resid 479 through 483 removed outlier: 6.159A pdb=" N CYS C 369 " --> pdb=" O VAL C 501 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N VAL C 503 " --> pdb=" O CYS C 369 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N ILE C 371 " --> pdb=" O VAL C 503 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N VAL C 333 " --> pdb=" O SER C 368 " (cutoff:3.500A) removed outlier: 8.202A pdb=" N TYR C 370 " --> pdb=" O VAL C 333 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N ILE C 335 " --> pdb=" O TYR C 370 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N SER C 372 " --> pdb=" O ILE C 335 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N VAL C 337 " --> pdb=" O SER C 372 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N ASP C 334 " --> pdb=" O LEU C 537 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N LEU C 539 " --> pdb=" O ASP C 334 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N PHE C 336 " --> pdb=" O LEU C 539 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N CYS C 613 " --> pdb=" O ASN C 538 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N CYS C 568 " --> pdb=" O ARG C 616 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N ILE C 757 " --> pdb=" O CYS C 568 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N VAL C 570 " --> pdb=" O ILE C 757 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 543 through 545 removed outlier: 6.523A pdb=" N ARG C 575 " --> pdb=" O GLY C 768 " (cutoff:3.500A) 854 hydrogen bonds defined for protein. 2535 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: 3.38 Time building geometry restraints manager: 2.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4240 1.33 - 1.45: 3918 1.45 - 1.57: 9863 1.57 - 1.69: 0 1.69 - 1.81: 165 Bond restraints: 18186 Sorted by residual: bond pdb=" C5 BGC H 2 " pdb=" O5 BGC H 2 " ideal model delta sigma weight residual 1.411 1.437 -0.026 2.00e-02 2.50e+03 1.64e+00 bond pdb=" C5 BGC G 1 " pdb=" O5 BGC G 1 " ideal model delta sigma weight residual 1.411 1.436 -0.025 2.00e-02 2.50e+03 1.62e+00 bond pdb=" C5 BGC E 2 " pdb=" O5 BGC E 2 " ideal model delta sigma weight residual 1.411 1.436 -0.025 2.00e-02 2.50e+03 1.61e+00 bond pdb=" C5 BGC I 2 " pdb=" O5 BGC I 2 " ideal model delta sigma weight residual 1.411 1.436 -0.025 2.00e-02 2.50e+03 1.58e+00 bond pdb=" C5 BGC F 2 " pdb=" O5 BGC F 2 " ideal model delta sigma weight residual 1.411 1.436 -0.025 2.00e-02 2.50e+03 1.58e+00 ... (remaining 18181 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.59: 23767 1.59 - 3.18: 801 3.18 - 4.78: 95 4.78 - 6.37: 39 6.37 - 7.96: 15 Bond angle restraints: 24717 Sorted by residual: angle pdb=" CA LYS A 682 " pdb=" CB LYS A 682 " pdb=" CG LYS A 682 " ideal model delta sigma weight residual 114.10 108.27 5.83 2.00e+00 2.50e-01 8.49e+00 angle pdb=" CA LYS C 682 " pdb=" CB LYS C 682 " pdb=" CG LYS C 682 " ideal model delta sigma weight residual 114.10 108.30 5.80 2.00e+00 2.50e-01 8.40e+00 angle pdb=" CA LYS B 682 " pdb=" CB LYS B 682 " pdb=" CG LYS B 682 " ideal model delta sigma weight residual 114.10 108.32 5.78 2.00e+00 2.50e-01 8.37e+00 angle pdb=" NE ARG C 432 " pdb=" CZ ARG C 432 " pdb=" NH2 ARG C 432 " ideal model delta sigma weight residual 119.20 121.63 -2.43 9.00e-01 1.23e+00 7.31e+00 angle pdb=" NE ARG A 432 " pdb=" CZ ARG A 432 " pdb=" NH2 ARG A 432 " ideal model delta sigma weight residual 119.20 121.62 -2.42 9.00e-01 1.23e+00 7.22e+00 ... (remaining 24712 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.83: 10169 21.83 - 43.66: 545 43.66 - 65.49: 107 65.49 - 87.32: 27 87.32 - 109.15: 24 Dihedral angle restraints: 10872 sinusoidal: 4554 harmonic: 6318 Sorted by residual: dihedral pdb=" C4 BGC E 1 " pdb=" C2 BGC E 1 " pdb=" C3 BGC E 1 " pdb=" O2 BGC E 1 " ideal model delta sinusoidal sigma weight residual 174.54 65.39 109.15 1 3.00e+01 1.11e-03 1.42e+01 dihedral pdb=" C4 BGC I 1 " pdb=" C2 BGC I 1 " pdb=" C3 BGC I 1 " pdb=" O2 BGC I 1 " ideal model delta sinusoidal sigma weight residual 174.54 65.40 109.14 1 3.00e+01 1.11e-03 1.42e+01 dihedral pdb=" C4 BGC G 1 " pdb=" C2 BGC G 1 " pdb=" C3 BGC G 1 " pdb=" O2 BGC G 1 " ideal model delta sinusoidal sigma weight residual 174.54 65.44 109.10 1 3.00e+01 1.11e-03 1.42e+01 ... (remaining 10869 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 2072 0.048 - 0.097: 538 0.097 - 0.145: 99 0.145 - 0.193: 15 0.193 - 0.241: 3 Chirality restraints: 2727 Sorted by residual: chirality pdb=" CB ILE C 367 " pdb=" CA ILE C 367 " pdb=" CG1 ILE C 367 " pdb=" CG2 ILE C 367 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.24 2.00e-01 2.50e+01 1.46e+00 chirality pdb=" CB ILE A 367 " pdb=" CA ILE A 367 " pdb=" CG1 ILE A 367 " pdb=" CG2 ILE A 367 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.24 2.00e-01 2.50e+01 1.45e+00 chirality pdb=" CB ILE B 367 " pdb=" CA ILE B 367 " pdb=" CG1 ILE B 367 " pdb=" CG2 ILE B 367 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.24 2.00e-01 2.50e+01 1.39e+00 ... (remaining 2724 not shown) Planarity restraints: 3081 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 306 " 0.013 2.00e-02 2.50e+03 1.48e-02 3.84e+00 pdb=" CG PHE B 306 " -0.034 2.00e-02 2.50e+03 pdb=" CD1 PHE B 306 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE B 306 " 0.010 2.00e-02 2.50e+03 pdb=" CE1 PHE B 306 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE B 306 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE B 306 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 306 " -0.012 2.00e-02 2.50e+03 1.47e-02 3.76e+00 pdb=" CG PHE C 306 " 0.034 2.00e-02 2.50e+03 pdb=" CD1 PHE C 306 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 PHE C 306 " -0.010 2.00e-02 2.50e+03 pdb=" CE1 PHE C 306 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE C 306 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE C 306 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 306 " 0.012 2.00e-02 2.50e+03 1.45e-02 3.67e+00 pdb=" CG PHE A 306 " -0.033 2.00e-02 2.50e+03 pdb=" CD1 PHE A 306 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE A 306 " 0.010 2.00e-02 2.50e+03 pdb=" CE1 PHE A 306 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 306 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE A 306 " 0.002 2.00e-02 2.50e+03 ... (remaining 3078 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 177 2.68 - 3.23: 17442 3.23 - 3.79: 26599 3.79 - 4.34: 35443 4.34 - 4.90: 57359 Nonbonded interactions: 137020 Sorted by model distance: nonbonded pdb=" O ALA C 331 " pdb=" OH TYR C 362 " model vdw 2.124 3.040 nonbonded pdb=" O ALA B 331 " pdb=" OH TYR B 362 " model vdw 2.124 3.040 nonbonded pdb=" O ALA A 331 " pdb=" OH TYR A 362 " model vdw 2.125 3.040 nonbonded pdb=" OE1 GLU A 723 " pdb=" OH TYR A 736 " model vdw 2.193 3.040 nonbonded pdb=" OE1 GLU B 723 " pdb=" OH TYR B 736 " model vdw 2.193 3.040 ... (remaining 137015 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 2.160 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: 0.040 Extract box with map and model: 0.320 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 18.550 Find NCS groups from input model: 0.240 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: 0.010 Load rotamer database and sin/cos tables:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7403 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 18192 Z= 0.160 Angle : 0.693 7.960 24735 Z= 0.365 Chirality : 0.044 0.241 2727 Planarity : 0.005 0.058 3081 Dihedral : 15.383 109.149 6804 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.77 % Favored : 92.23 % Rotamer: Outliers : 0.79 % Allowed : 1.43 % Favored : 97.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.11 (0.18), residues: 2163 helix: 0.90 (0.15), residues: 1167 sheet: -1.15 (0.38), residues: 147 loop : -1.21 (0.21), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 795 TYR 0.020 0.002 TYR B 758 PHE 0.034 0.001 PHE B 306 TRP 0.024 0.001 TRP C 800 HIS 0.003 0.001 HIS A 986 Details of bonding type rmsd covalent geometry : bond 0.00328 (18186) covalent geometry : angle 0.69063 (24717) hydrogen bonds : bond 0.12407 ( 854) hydrogen bonds : angle 5.06698 ( 2535) link_BETA1-4 : bond 0.00218 ( 6) link_BETA1-4 : angle 2.12977 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 1890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 330 time to evaluate : 0.650 Fit side-chains REVERT: A 237 GLN cc_start: 0.7938 (mp10) cc_final: 0.7581 (mp10) REVERT: A 241 ARG cc_start: 0.7155 (ttp-110) cc_final: 0.6884 (ttm110) REVERT: A 360 MET cc_start: 0.8296 (ttp) cc_final: 0.7985 (ttp) REVERT: A 434 MET cc_start: 0.8289 (tpp) cc_final: 0.8002 (tpp) REVERT: A 908 LYS cc_start: 0.7816 (ttpt) cc_final: 0.6755 (ttpt) REVERT: B 237 GLN cc_start: 0.7931 (mp10) cc_final: 0.7305 (mp10) REVERT: B 343 MET cc_start: 0.7835 (mmm) cc_final: 0.7564 (mmm) REVERT: B 389 GLU cc_start: 0.8246 (mm-30) cc_final: 0.7395 (mm-30) REVERT: B 474 LYS cc_start: 0.7779 (mttp) cc_final: 0.7483 (mmmm) REVERT: B 555 MET cc_start: 0.8951 (mmt) cc_final: 0.8712 (mmm) REVERT: B 786 LEU cc_start: 0.8392 (tp) cc_final: 0.8119 (tp) REVERT: B 847 MET cc_start: 0.9007 (pmm) cc_final: 0.8315 (pmm) REVERT: C 237 GLN cc_start: 0.8099 (mp10) cc_final: 0.7809 (mp10) REVERT: C 313 TYR cc_start: 0.8073 (m-10) cc_final: 0.7475 (m-80) REVERT: C 323 ARG cc_start: 0.7563 (ptt180) cc_final: 0.7233 (ptt90) REVERT: C 474 LYS cc_start: 0.7801 (mttp) cc_final: 0.7565 (mmtp) REVERT: C 795 ARG cc_start: 0.7160 (ptt-90) cc_final: 0.6827 (ptt-90) outliers start: 15 outliers final: 3 residues processed: 335 average time/residue: 0.1499 time to fit residues: 74.4434 Evaluate side-chains 287 residues out of total 1890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 284 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 493 GLU Chi-restraints excluded: chain B residue 493 GLU Chi-restraints excluded: chain C residue 493 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 0.7980 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 0.0370 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 0.3980 chunk 103 optimal weight: 0.7980 chunk 200 optimal weight: 0.0370 chunk 212 optimal weight: 9.9990 chunk 77 optimal weight: 2.9990 overall best weight: 0.4136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 513 HIS ** A 898 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 486 GLN ** B 898 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 898 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.192258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.143679 restraints weight = 21237.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.142839 restraints weight = 17914.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.143542 restraints weight = 21336.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.144541 restraints weight = 12408.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.144977 restraints weight = 10779.812| |-----------------------------------------------------------------------------| r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 moved from start: 0.1017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 18192 Z= 0.127 Angle : 0.618 7.586 24735 Z= 0.305 Chirality : 0.043 0.187 2727 Planarity : 0.004 0.045 3081 Dihedral : 9.684 93.957 2625 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 1.01 % Allowed : 7.35 % Favored : 91.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.10 (0.18), residues: 2163 helix: 1.11 (0.15), residues: 1173 sheet: -1.11 (0.37), residues: 162 loop : -1.17 (0.20), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 795 TYR 0.017 0.001 TYR C 758 PHE 0.027 0.001 PHE B 306 TRP 0.012 0.001 TRP A 800 HIS 0.004 0.001 HIS B 277 Details of bonding type rmsd covalent geometry : bond 0.00281 (18186) covalent geometry : angle 0.61423 (24717) hydrogen bonds : bond 0.04244 ( 854) hydrogen bonds : angle 4.22281 ( 2535) link_BETA1-4 : bond 0.00225 ( 6) link_BETA1-4 : angle 2.50768 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 1890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 316 time to evaluate : 0.645 Fit side-chains REVERT: A 237 GLN cc_start: 0.7861 (mp10) cc_final: 0.7497 (mp10) REVERT: A 360 MET cc_start: 0.8350 (ttp) cc_final: 0.8030 (ttp) REVERT: A 389 GLU cc_start: 0.8113 (mm-30) cc_final: 0.7590 (mm-30) REVERT: A 434 MET cc_start: 0.8371 (tpp) cc_final: 0.8069 (tpp) REVERT: A 493 GLU cc_start: 0.7858 (mm-30) cc_final: 0.7626 (mm-30) REVERT: A 527 SER cc_start: 0.8964 (m) cc_final: 0.8754 (m) REVERT: A 546 ASN cc_start: 0.8539 (t0) cc_final: 0.8209 (t0) REVERT: A 555 MET cc_start: 0.8914 (mmt) cc_final: 0.8305 (mmt) REVERT: B 389 GLU cc_start: 0.8036 (mm-30) cc_final: 0.7543 (mm-30) REVERT: B 527 SER cc_start: 0.9011 (m) cc_final: 0.8784 (m) REVERT: B 555 MET cc_start: 0.8910 (mmt) cc_final: 0.8599 (mmm) REVERT: B 807 LYS cc_start: 0.7175 (mttt) cc_final: 0.6584 (mtpp) REVERT: C 474 LYS cc_start: 0.7823 (mttp) cc_final: 0.7602 (mmtp) REVERT: C 692 THR cc_start: 0.8130 (m) cc_final: 0.7798 (p) REVERT: C 795 ARG cc_start: 0.7108 (ptt-90) cc_final: 0.6765 (ptt-90) REVERT: C 847 MET cc_start: 0.8894 (pmm) cc_final: 0.8458 (pmm) REVERT: C 908 LYS cc_start: 0.7803 (ttpt) cc_final: 0.7554 (ttpt) outliers start: 19 outliers final: 11 residues processed: 320 average time/residue: 0.1435 time to fit residues: 68.5007 Evaluate side-chains 294 residues out of total 1890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 283 time to evaluate : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 490 HIS Chi-restraints excluded: chain A residue 611 THR Chi-restraints excluded: chain A residue 718 ILE Chi-restraints excluded: chain B residue 490 HIS Chi-restraints excluded: chain B residue 679 ASN Chi-restraints excluded: chain B residue 694 THR Chi-restraints excluded: chain C residue 443 VAL Chi-restraints excluded: chain C residue 679 ASN Chi-restraints excluded: chain C residue 694 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 177 optimal weight: 0.8980 chunk 205 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 chunk 83 optimal weight: 0.9980 chunk 28 optimal weight: 0.9990 chunk 144 optimal weight: 4.9990 chunk 84 optimal weight: 0.9990 chunk 102 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 513 HIS ** A 898 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 486 GLN ** B 898 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 898 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.188947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.140110 restraints weight = 21621.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.135286 restraints weight = 16840.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.136811 restraints weight = 21819.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.138207 restraints weight = 12256.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.141078 restraints weight = 10250.968| |-----------------------------------------------------------------------------| r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7480 moved from start: 0.1441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 18192 Z= 0.152 Angle : 0.628 8.248 24735 Z= 0.305 Chirality : 0.043 0.173 2727 Planarity : 0.004 0.037 3081 Dihedral : 6.570 48.419 2616 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 1.75 % Allowed : 10.00 % Favored : 88.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.22 (0.18), residues: 2163 helix: 1.23 (0.16), residues: 1176 sheet: -0.88 (0.38), residues: 165 loop : -1.21 (0.20), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 795 TYR 0.020 0.002 TYR B 758 PHE 0.023 0.001 PHE C 306 TRP 0.015 0.001 TRP B 800 HIS 0.006 0.001 HIS B 514 Details of bonding type rmsd covalent geometry : bond 0.00361 (18186) covalent geometry : angle 0.62197 (24717) hydrogen bonds : bond 0.04057 ( 854) hydrogen bonds : angle 4.08237 ( 2535) link_BETA1-4 : bond 0.00288 ( 6) link_BETA1-4 : angle 3.37598 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 1890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 305 time to evaluate : 0.764 Fit side-chains REVERT: A 237 GLN cc_start: 0.7901 (mp10) cc_final: 0.7354 (mp10) REVERT: A 360 MET cc_start: 0.8453 (ttp) cc_final: 0.8218 (ttp) REVERT: A 373 ASP cc_start: 0.8415 (t0) cc_final: 0.8162 (t0) REVERT: A 389 GLU cc_start: 0.8049 (mm-30) cc_final: 0.7680 (mm-30) REVERT: A 527 SER cc_start: 0.8927 (m) cc_final: 0.8662 (m) REVERT: A 546 ASN cc_start: 0.8535 (t0) cc_final: 0.8153 (t0) REVERT: A 886 ASN cc_start: 0.8328 (t0) cc_final: 0.7733 (t0) REVERT: B 237 GLN cc_start: 0.7907 (mp10) cc_final: 0.7427 (mp10) REVERT: B 389 GLU cc_start: 0.7998 (mm-30) cc_final: 0.7596 (mm-30) REVERT: B 527 SER cc_start: 0.9047 (m) cc_final: 0.8830 (m) REVERT: B 807 LYS cc_start: 0.7118 (mttt) cc_final: 0.6520 (mtpp) REVERT: C 237 GLN cc_start: 0.8043 (mp10) cc_final: 0.7435 (mp10) REVERT: C 403 ILE cc_start: 0.8286 (mm) cc_final: 0.7926 (mm) REVERT: C 474 LYS cc_start: 0.7821 (mttp) cc_final: 0.7617 (mmtp) REVERT: C 786 LEU cc_start: 0.8426 (OUTLIER) cc_final: 0.8155 (tp) REVERT: C 847 MET cc_start: 0.8980 (pmm) cc_final: 0.8705 (pmm) outliers start: 33 outliers final: 28 residues processed: 314 average time/residue: 0.1391 time to fit residues: 65.9828 Evaluate side-chains 304 residues out of total 1890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 275 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 462 MET Chi-restraints excluded: chain A residue 611 THR Chi-restraints excluded: chain A residue 684 PHE Chi-restraints excluded: chain A residue 718 ILE Chi-restraints excluded: chain A residue 726 THR Chi-restraints excluded: chain A residue 891 VAL Chi-restraints excluded: chain B residue 421 ASP Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain B residue 679 ASN Chi-restraints excluded: chain B residue 684 PHE Chi-restraints excluded: chain B residue 694 THR Chi-restraints excluded: chain B residue 719 SER Chi-restraints excluded: chain B residue 726 THR Chi-restraints excluded: chain B residue 773 ASN Chi-restraints excluded: chain B residue 940 LEU Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain C residue 443 VAL Chi-restraints excluded: chain C residue 490 HIS Chi-restraints excluded: chain C residue 679 ASN Chi-restraints excluded: chain C residue 684 PHE Chi-restraints excluded: chain C residue 694 THR Chi-restraints excluded: chain C residue 719 SER Chi-restraints excluded: chain C residue 726 THR Chi-restraints excluded: chain C residue 773 ASN Chi-restraints excluded: chain C residue 786 LEU Chi-restraints excluded: chain C residue 891 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 150 optimal weight: 0.0980 chunk 35 optimal weight: 3.9990 chunk 18 optimal weight: 0.0030 chunk 147 optimal weight: 0.5980 chunk 127 optimal weight: 3.9990 chunk 63 optimal weight: 0.0980 chunk 132 optimal weight: 6.9990 chunk 1 optimal weight: 7.9990 chunk 144 optimal weight: 4.9990 chunk 213 optimal weight: 5.9990 chunk 34 optimal weight: 4.9990 overall best weight: 0.9592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 513 HIS ** A 898 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 486 GLN B 677 GLN ** B 898 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 898 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.188200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.139431 restraints weight = 21397.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.134753 restraints weight = 16861.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.136055 restraints weight = 22254.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.138099 restraints weight = 12256.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.139986 restraints weight = 9719.296| |-----------------------------------------------------------------------------| r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.1735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 18192 Z= 0.148 Angle : 0.607 7.828 24735 Z= 0.296 Chirality : 0.043 0.188 2727 Planarity : 0.004 0.042 3081 Dihedral : 5.621 46.592 2616 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 2.43 % Allowed : 11.85 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.35 (0.18), residues: 2163 helix: 1.38 (0.16), residues: 1158 sheet: -0.73 (0.39), residues: 165 loop : -1.18 (0.20), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 565 TYR 0.016 0.002 TYR C 758 PHE 0.014 0.001 PHE A 306 TRP 0.014 0.001 TRP C 800 HIS 0.004 0.001 HIS A 514 Details of bonding type rmsd covalent geometry : bond 0.00353 (18186) covalent geometry : angle 0.59921 (24717) hydrogen bonds : bond 0.03883 ( 854) hydrogen bonds : angle 3.99281 ( 2535) link_BETA1-4 : bond 0.00465 ( 6) link_BETA1-4 : angle 3.60518 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 1890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 294 time to evaluate : 0.655 Fit side-chains revert: symmetry clash REVERT: A 237 GLN cc_start: 0.7906 (mp10) cc_final: 0.7437 (mp10) REVERT: A 360 MET cc_start: 0.8462 (ttp) cc_final: 0.8216 (ttp) REVERT: A 373 ASP cc_start: 0.8406 (t0) cc_final: 0.8064 (t0) REVERT: A 389 GLU cc_start: 0.8030 (mm-30) cc_final: 0.7646 (mm-30) REVERT: A 527 SER cc_start: 0.8856 (m) cc_final: 0.8584 (m) REVERT: A 546 ASN cc_start: 0.8511 (t0) cc_final: 0.8212 (t0) REVERT: A 675 MET cc_start: 0.6262 (tmm) cc_final: 0.6048 (tmm) REVERT: A 886 ASN cc_start: 0.8632 (t0) cc_final: 0.8082 (t0) REVERT: B 237 GLN cc_start: 0.8008 (mp10) cc_final: 0.7543 (mp10) REVERT: B 373 ASP cc_start: 0.8534 (t0) cc_final: 0.8044 (t70) REVERT: B 389 GLU cc_start: 0.7951 (mm-30) cc_final: 0.7576 (mm-30) REVERT: B 807 LYS cc_start: 0.7192 (mttt) cc_final: 0.6599 (mtpp) REVERT: C 237 GLN cc_start: 0.8025 (mp10) cc_final: 0.7600 (pm20) REVERT: C 403 ILE cc_start: 0.8269 (mm) cc_final: 0.7907 (mm) REVERT: C 474 LYS cc_start: 0.7813 (mttp) cc_final: 0.7602 (mmtp) REVERT: C 847 MET cc_start: 0.8963 (pmm) cc_final: 0.8730 (pmm) REVERT: C 908 LYS cc_start: 0.8310 (ttpt) cc_final: 0.7930 (tttm) outliers start: 46 outliers final: 32 residues processed: 314 average time/residue: 0.1383 time to fit residues: 65.8533 Evaluate side-chains 312 residues out of total 1890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 280 time to evaluate : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 462 MET Chi-restraints excluded: chain A residue 479 MET Chi-restraints excluded: chain A residue 611 THR Chi-restraints excluded: chain A residue 684 PHE Chi-restraints excluded: chain A residue 694 THR Chi-restraints excluded: chain A residue 718 ILE Chi-restraints excluded: chain A residue 719 SER Chi-restraints excluded: chain A residue 726 THR Chi-restraints excluded: chain A residue 891 VAL Chi-restraints excluded: chain B residue 600 LEU Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain B residue 679 ASN Chi-restraints excluded: chain B residue 684 PHE Chi-restraints excluded: chain B residue 694 THR Chi-restraints excluded: chain B residue 719 SER Chi-restraints excluded: chain B residue 726 THR Chi-restraints excluded: chain B residue 773 ASN Chi-restraints excluded: chain B residue 940 LEU Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain C residue 443 VAL Chi-restraints excluded: chain C residue 455 VAL Chi-restraints excluded: chain C residue 490 HIS Chi-restraints excluded: chain C residue 611 THR Chi-restraints excluded: chain C residue 684 PHE Chi-restraints excluded: chain C residue 694 THR Chi-restraints excluded: chain C residue 715 ILE Chi-restraints excluded: chain C residue 719 SER Chi-restraints excluded: chain C residue 726 THR Chi-restraints excluded: chain C residue 891 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 189 optimal weight: 0.8980 chunk 165 optimal weight: 0.9980 chunk 96 optimal weight: 0.4980 chunk 129 optimal weight: 4.9990 chunk 44 optimal weight: 0.0770 chunk 195 optimal weight: 3.9990 chunk 119 optimal weight: 0.6980 chunk 11 optimal weight: 0.0770 chunk 15 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 121 optimal weight: 6.9990 overall best weight: 0.4496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 513 HIS ** A 898 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 898 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 898 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.190348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.141505 restraints weight = 21448.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.137300 restraints weight = 16306.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.138524 restraints weight = 22010.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.140567 restraints weight = 12308.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.143000 restraints weight = 9830.711| |-----------------------------------------------------------------------------| r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7445 moved from start: 0.1899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 18192 Z= 0.112 Angle : 0.577 9.019 24735 Z= 0.278 Chirality : 0.041 0.187 2727 Planarity : 0.004 0.037 3081 Dihedral : 5.213 46.145 2616 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 2.06 % Allowed : 12.80 % Favored : 85.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.58 (0.18), residues: 2163 helix: 1.55 (0.16), residues: 1158 sheet: -0.56 (0.40), residues: 165 loop : -1.07 (0.20), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 565 TYR 0.017 0.001 TYR A 621 PHE 0.011 0.001 PHE B 397 TRP 0.014 0.001 TRP C 800 HIS 0.003 0.001 HIS B 514 Details of bonding type rmsd covalent geometry : bond 0.00254 (18186) covalent geometry : angle 0.57092 (24717) hydrogen bonds : bond 0.03385 ( 854) hydrogen bonds : angle 3.80951 ( 2535) link_BETA1-4 : bond 0.00581 ( 6) link_BETA1-4 : angle 3.02536 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 1890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 312 time to evaluate : 0.617 Fit side-chains REVERT: A 237 GLN cc_start: 0.7849 (mp10) cc_final: 0.7394 (mp10) REVERT: A 360 MET cc_start: 0.8352 (ttp) cc_final: 0.8043 (ttp) REVERT: A 389 GLU cc_start: 0.8032 (mm-30) cc_final: 0.7630 (mm-30) REVERT: A 546 ASN cc_start: 0.8526 (t0) cc_final: 0.8190 (t0) REVERT: A 694 THR cc_start: 0.8664 (OUTLIER) cc_final: 0.8423 (t) REVERT: A 886 ASN cc_start: 0.8637 (t0) cc_final: 0.8090 (t0) REVERT: B 237 GLN cc_start: 0.7979 (mp10) cc_final: 0.7422 (mp10) REVERT: B 389 GLU cc_start: 0.7946 (mm-30) cc_final: 0.7585 (mm-30) REVERT: B 807 LYS cc_start: 0.7120 (mttt) cc_final: 0.6536 (mtpp) REVERT: C 237 GLN cc_start: 0.7933 (mp10) cc_final: 0.7640 (pm20) REVERT: C 373 ASP cc_start: 0.8252 (t0) cc_final: 0.7914 (t0) REVERT: C 403 ILE cc_start: 0.8149 (mm) cc_final: 0.7738 (mm) REVERT: C 908 LYS cc_start: 0.8305 (ttpt) cc_final: 0.8017 (tttm) outliers start: 39 outliers final: 32 residues processed: 331 average time/residue: 0.1404 time to fit residues: 70.3925 Evaluate side-chains 317 residues out of total 1890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 284 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 462 MET Chi-restraints excluded: chain A residue 479 MET Chi-restraints excluded: chain A residue 603 ILE Chi-restraints excluded: chain A residue 611 THR Chi-restraints excluded: chain A residue 679 ASN Chi-restraints excluded: chain A residue 684 PHE Chi-restraints excluded: chain A residue 694 THR Chi-restraints excluded: chain A residue 718 ILE Chi-restraints excluded: chain A residue 719 SER Chi-restraints excluded: chain A residue 891 VAL Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 600 LEU Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain B residue 679 ASN Chi-restraints excluded: chain B residue 684 PHE Chi-restraints excluded: chain B residue 694 THR Chi-restraints excluded: chain B residue 718 ILE Chi-restraints excluded: chain B residue 719 SER Chi-restraints excluded: chain B residue 773 ASN Chi-restraints excluded: chain C residue 443 VAL Chi-restraints excluded: chain C residue 490 HIS Chi-restraints excluded: chain C residue 600 LEU Chi-restraints excluded: chain C residue 603 ILE Chi-restraints excluded: chain C residue 611 THR Chi-restraints excluded: chain C residue 679 ASN Chi-restraints excluded: chain C residue 684 PHE Chi-restraints excluded: chain C residue 694 THR Chi-restraints excluded: chain C residue 719 SER Chi-restraints excluded: chain C residue 773 ASN Chi-restraints excluded: chain C residue 891 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 210 optimal weight: 8.9990 chunk 117 optimal weight: 0.7980 chunk 12 optimal weight: 0.0000 chunk 161 optimal weight: 0.0010 chunk 162 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 17 optimal weight: 0.0870 chunk 164 optimal weight: 0.8980 chunk 32 optimal weight: 0.8980 chunk 163 optimal weight: 0.9980 overall best weight: 0.3568 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 513 HIS ** A 898 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 898 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 898 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.190914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.141780 restraints weight = 21320.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.137759 restraints weight = 16397.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.139126 restraints weight = 21288.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.141033 restraints weight = 12377.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.141507 restraints weight = 10111.146| |-----------------------------------------------------------------------------| r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7458 moved from start: 0.2073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 18192 Z= 0.107 Angle : 0.570 7.938 24735 Z= 0.275 Chirality : 0.041 0.188 2727 Planarity : 0.004 0.084 3081 Dihedral : 5.066 58.692 2616 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 2.01 % Allowed : 13.54 % Favored : 84.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.73 (0.18), residues: 2163 helix: 1.67 (0.16), residues: 1158 sheet: -0.52 (0.40), residues: 165 loop : -0.99 (0.20), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 323 TYR 0.017 0.001 TYR A 621 PHE 0.010 0.001 PHE B 397 TRP 0.013 0.001 TRP C 800 HIS 0.003 0.001 HIS A 514 Details of bonding type rmsd covalent geometry : bond 0.00245 (18186) covalent geometry : angle 0.56448 (24717) hydrogen bonds : bond 0.03194 ( 854) hydrogen bonds : angle 3.70100 ( 2535) link_BETA1-4 : bond 0.00590 ( 6) link_BETA1-4 : angle 2.88580 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 1890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 292 time to evaluate : 0.588 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 237 GLN cc_start: 0.7878 (mp10) cc_final: 0.7394 (mp10) REVERT: A 360 MET cc_start: 0.8306 (ttp) cc_final: 0.7982 (ttp) REVERT: A 389 GLU cc_start: 0.7984 (mm-30) cc_final: 0.7581 (mm-30) REVERT: A 546 ASN cc_start: 0.8517 (t0) cc_final: 0.8197 (t0) REVERT: A 694 THR cc_start: 0.8646 (OUTLIER) cc_final: 0.8406 (t) REVERT: A 886 ASN cc_start: 0.8633 (t0) cc_final: 0.7946 (t0) REVERT: B 237 GLN cc_start: 0.7936 (mp10) cc_final: 0.7501 (mp10) REVERT: B 323 ARG cc_start: 0.7366 (ptt-90) cc_final: 0.7018 (ptt90) REVERT: B 389 GLU cc_start: 0.7888 (mm-30) cc_final: 0.7493 (mm-30) REVERT: B 807 LYS cc_start: 0.7224 (mttt) cc_final: 0.6606 (mtpp) REVERT: B 847 MET cc_start: 0.8920 (pmm) cc_final: 0.8627 (pmm) REVERT: C 237 GLN cc_start: 0.7981 (mp10) cc_final: 0.7687 (pm20) REVERT: C 389 GLU cc_start: 0.8192 (mm-30) cc_final: 0.7955 (mm-30) outliers start: 38 outliers final: 30 residues processed: 311 average time/residue: 0.1410 time to fit residues: 65.6966 Evaluate side-chains 306 residues out of total 1890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 275 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 462 MET Chi-restraints excluded: chain A residue 479 MET Chi-restraints excluded: chain A residue 611 THR Chi-restraints excluded: chain A residue 679 ASN Chi-restraints excluded: chain A residue 684 PHE Chi-restraints excluded: chain A residue 694 THR Chi-restraints excluded: chain A residue 718 ILE Chi-restraints excluded: chain A residue 719 SER Chi-restraints excluded: chain A residue 891 VAL Chi-restraints excluded: chain B residue 241 ARG Chi-restraints excluded: chain B residue 600 LEU Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain B residue 679 ASN Chi-restraints excluded: chain B residue 684 PHE Chi-restraints excluded: chain B residue 694 THR Chi-restraints excluded: chain B residue 719 SER Chi-restraints excluded: chain C residue 443 VAL Chi-restraints excluded: chain C residue 455 VAL Chi-restraints excluded: chain C residue 490 HIS Chi-restraints excluded: chain C residue 600 LEU Chi-restraints excluded: chain C residue 603 ILE Chi-restraints excluded: chain C residue 611 THR Chi-restraints excluded: chain C residue 679 ASN Chi-restraints excluded: chain C residue 684 PHE Chi-restraints excluded: chain C residue 694 THR Chi-restraints excluded: chain C residue 719 SER Chi-restraints excluded: chain C residue 891 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 118 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 179 optimal weight: 3.9990 chunk 120 optimal weight: 0.9980 chunk 163 optimal weight: 0.6980 chunk 119 optimal weight: 0.9990 chunk 50 optimal weight: 0.8980 chunk 85 optimal weight: 0.9980 chunk 134 optimal weight: 2.9990 chunk 214 optimal weight: 20.0000 chunk 64 optimal weight: 3.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 513 HIS ** A 898 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 898 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 898 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.188546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.138796 restraints weight = 21454.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.134871 restraints weight = 16249.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.136041 restraints weight = 20893.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.137510 restraints weight = 12636.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.137974 restraints weight = 10604.964| |-----------------------------------------------------------------------------| r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.2172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 18192 Z= 0.144 Angle : 0.601 10.270 24735 Z= 0.291 Chirality : 0.042 0.194 2727 Planarity : 0.004 0.101 3081 Dihedral : 4.827 44.743 2616 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 2.28 % Allowed : 13.97 % Favored : 83.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.69 (0.18), residues: 2163 helix: 1.65 (0.16), residues: 1158 sheet: -0.58 (0.38), residues: 165 loop : -1.03 (0.20), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 323 TYR 0.021 0.002 TYR A 621 PHE 0.010 0.001 PHE B 483 TRP 0.014 0.001 TRP B 800 HIS 0.005 0.001 HIS A 514 Details of bonding type rmsd covalent geometry : bond 0.00348 (18186) covalent geometry : angle 0.59494 (24717) hydrogen bonds : bond 0.03529 ( 854) hydrogen bonds : angle 3.76735 ( 2535) link_BETA1-4 : bond 0.00486 ( 6) link_BETA1-4 : angle 3.17289 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 1890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 284 time to evaluate : 0.679 Fit side-chains REVERT: A 237 GLN cc_start: 0.7935 (mp10) cc_final: 0.7556 (pm20) REVERT: A 360 MET cc_start: 0.8432 (ttp) cc_final: 0.8167 (ttp) REVERT: A 389 GLU cc_start: 0.8015 (mm-30) cc_final: 0.7685 (mm-30) REVERT: A 546 ASN cc_start: 0.8507 (t0) cc_final: 0.8175 (t0) REVERT: A 886 ASN cc_start: 0.8668 (t0) cc_final: 0.7990 (t0) REVERT: B 237 GLN cc_start: 0.8014 (mp10) cc_final: 0.7562 (mp10) REVERT: B 323 ARG cc_start: 0.7438 (ptt-90) cc_final: 0.7152 (ptt90) REVERT: B 389 GLU cc_start: 0.7937 (mm-30) cc_final: 0.7534 (mm-30) REVERT: B 807 LYS cc_start: 0.7245 (mttt) cc_final: 0.6662 (mtpp) REVERT: C 237 GLN cc_start: 0.8049 (mp10) cc_final: 0.7741 (pm20) REVERT: C 386 GLU cc_start: 0.7034 (mm-30) cc_final: 0.6787 (tp30) REVERT: C 403 ILE cc_start: 0.8292 (mm) cc_final: 0.7915 (mm) outliers start: 43 outliers final: 35 residues processed: 303 average time/residue: 0.1353 time to fit residues: 62.3003 Evaluate side-chains 313 residues out of total 1890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 278 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 462 MET Chi-restraints excluded: chain A residue 479 MET Chi-restraints excluded: chain A residue 611 THR Chi-restraints excluded: chain A residue 679 ASN Chi-restraints excluded: chain A residue 684 PHE Chi-restraints excluded: chain A residue 694 THR Chi-restraints excluded: chain A residue 718 ILE Chi-restraints excluded: chain A residue 726 THR Chi-restraints excluded: chain A residue 842 THR Chi-restraints excluded: chain A residue 891 VAL Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 490 HIS Chi-restraints excluded: chain B residue 600 LEU Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain B residue 679 ASN Chi-restraints excluded: chain B residue 684 PHE Chi-restraints excluded: chain B residue 694 THR Chi-restraints excluded: chain B residue 719 SER Chi-restraints excluded: chain B residue 726 THR Chi-restraints excluded: chain B residue 940 LEU Chi-restraints excluded: chain C residue 443 VAL Chi-restraints excluded: chain C residue 455 VAL Chi-restraints excluded: chain C residue 490 HIS Chi-restraints excluded: chain C residue 600 LEU Chi-restraints excluded: chain C residue 611 THR Chi-restraints excluded: chain C residue 679 ASN Chi-restraints excluded: chain C residue 684 PHE Chi-restraints excluded: chain C residue 694 THR Chi-restraints excluded: chain C residue 719 SER Chi-restraints excluded: chain C residue 726 THR Chi-restraints excluded: chain C residue 891 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 26 optimal weight: 0.0170 chunk 15 optimal weight: 1.9990 chunk 211 optimal weight: 5.9990 chunk 77 optimal weight: 3.9990 chunk 130 optimal weight: 0.9990 chunk 163 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 6 optimal weight: 0.3980 chunk 21 optimal weight: 0.5980 overall best weight: 0.6020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 513 HIS ** A 898 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 898 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 898 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.189894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.141181 restraints weight = 21459.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.137210 restraints weight = 16922.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.138637 restraints weight = 21680.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.139989 restraints weight = 12578.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.142993 restraints weight = 10585.813| |-----------------------------------------------------------------------------| r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7442 moved from start: 0.2269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 18192 Z= 0.120 Angle : 0.590 9.389 24735 Z= 0.285 Chirality : 0.041 0.196 2727 Planarity : 0.004 0.084 3081 Dihedral : 4.616 57.639 2616 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 1.96 % Allowed : 14.87 % Favored : 83.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.78 (0.18), residues: 2163 helix: 1.76 (0.16), residues: 1155 sheet: -0.53 (0.38), residues: 165 loop : -1.03 (0.20), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 323 TYR 0.016 0.001 TYR A 621 PHE 0.011 0.001 PHE B 397 TRP 0.015 0.001 TRP A 784 HIS 0.004 0.001 HIS B 514 Details of bonding type rmsd covalent geometry : bond 0.00284 (18186) covalent geometry : angle 0.58589 (24717) hydrogen bonds : bond 0.03311 ( 854) hydrogen bonds : angle 3.70992 ( 2535) link_BETA1-4 : bond 0.00470 ( 6) link_BETA1-4 : angle 2.78824 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 1890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 286 time to evaluate : 0.665 Fit side-chains REVERT: A 237 GLN cc_start: 0.7844 (mp10) cc_final: 0.7524 (pm20) REVERT: A 360 MET cc_start: 0.8375 (ttp) cc_final: 0.8066 (ttp) REVERT: A 378 MET cc_start: 0.8071 (ttp) cc_final: 0.7861 (ttm) REVERT: A 389 GLU cc_start: 0.8016 (mm-30) cc_final: 0.7694 (mm-30) REVERT: A 546 ASN cc_start: 0.8526 (t0) cc_final: 0.8165 (t0) REVERT: A 675 MET cc_start: 0.6272 (tmm) cc_final: 0.5967 (tmm) REVERT: A 694 THR cc_start: 0.8619 (OUTLIER) cc_final: 0.8398 (t) REVERT: A 886 ASN cc_start: 0.8586 (t0) cc_final: 0.7940 (t0) REVERT: B 237 GLN cc_start: 0.7938 (mp10) cc_final: 0.7547 (mp10) REVERT: B 255 MET cc_start: 0.7108 (mtm) cc_final: 0.6904 (mtm) REVERT: B 323 ARG cc_start: 0.7440 (ptt-90) cc_final: 0.7177 (ptt90) REVERT: B 389 GLU cc_start: 0.7935 (mm-30) cc_final: 0.7532 (mm-30) REVERT: B 807 LYS cc_start: 0.7166 (mttt) cc_final: 0.6588 (mtpp) REVERT: B 847 MET cc_start: 0.8891 (pmm) cc_final: 0.8666 (pmm) REVERT: C 386 GLU cc_start: 0.7055 (mm-30) cc_final: 0.6777 (tp30) REVERT: C 403 ILE cc_start: 0.8124 (mm) cc_final: 0.7718 (mm) outliers start: 37 outliers final: 32 residues processed: 305 average time/residue: 0.1404 time to fit residues: 64.5414 Evaluate side-chains 311 residues out of total 1890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 278 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 462 MET Chi-restraints excluded: chain A residue 479 MET Chi-restraints excluded: chain A residue 611 THR Chi-restraints excluded: chain A residue 679 ASN Chi-restraints excluded: chain A residue 684 PHE Chi-restraints excluded: chain A residue 694 THR Chi-restraints excluded: chain A residue 718 ILE Chi-restraints excluded: chain A residue 842 THR Chi-restraints excluded: chain A residue 891 VAL Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 600 LEU Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain B residue 679 ASN Chi-restraints excluded: chain B residue 684 PHE Chi-restraints excluded: chain B residue 694 THR Chi-restraints excluded: chain B residue 719 SER Chi-restraints excluded: chain B residue 726 THR Chi-restraints excluded: chain B residue 842 THR Chi-restraints excluded: chain C residue 443 VAL Chi-restraints excluded: chain C residue 455 VAL Chi-restraints excluded: chain C residue 490 HIS Chi-restraints excluded: chain C residue 600 LEU Chi-restraints excluded: chain C residue 611 THR Chi-restraints excluded: chain C residue 679 ASN Chi-restraints excluded: chain C residue 684 PHE Chi-restraints excluded: chain C residue 694 THR Chi-restraints excluded: chain C residue 719 SER Chi-restraints excluded: chain C residue 842 THR Chi-restraints excluded: chain C residue 891 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 193 optimal weight: 1.9990 chunk 145 optimal weight: 0.9980 chunk 151 optimal weight: 2.9990 chunk 135 optimal weight: 7.9990 chunk 0 optimal weight: 5.9990 chunk 47 optimal weight: 0.5980 chunk 160 optimal weight: 1.9990 chunk 155 optimal weight: 0.6980 chunk 41 optimal weight: 0.8980 chunk 38 optimal weight: 0.7980 chunk 133 optimal weight: 6.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 513 HIS ** A 898 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 898 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 677 GLN ** C 898 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.188979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.139692 restraints weight = 21519.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.136287 restraints weight = 16849.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.137482 restraints weight = 21541.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.138777 restraints weight = 12967.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.139252 restraints weight = 11058.982| |-----------------------------------------------------------------------------| r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 0.2351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 18192 Z= 0.135 Angle : 0.608 11.431 24735 Z= 0.293 Chirality : 0.042 0.199 2727 Planarity : 0.004 0.082 3081 Dihedral : 4.403 45.539 2616 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 2.28 % Allowed : 14.92 % Favored : 82.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.78 (0.18), residues: 2163 helix: 1.77 (0.16), residues: 1155 sheet: -0.52 (0.38), residues: 165 loop : -1.05 (0.20), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 323 TYR 0.018 0.001 TYR A 621 PHE 0.010 0.001 PHE B 397 TRP 0.014 0.001 TRP B 800 HIS 0.004 0.001 HIS A 514 Details of bonding type rmsd covalent geometry : bond 0.00325 (18186) covalent geometry : angle 0.60334 (24717) hydrogen bonds : bond 0.03409 ( 854) hydrogen bonds : angle 3.72697 ( 2535) link_BETA1-4 : bond 0.00400 ( 6) link_BETA1-4 : angle 2.82876 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 1890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 284 time to evaluate : 0.634 Fit side-chains REVERT: A 237 GLN cc_start: 0.7909 (mp10) cc_final: 0.7583 (pm20) REVERT: A 360 MET cc_start: 0.8426 (ttp) cc_final: 0.8150 (ttp) REVERT: A 389 GLU cc_start: 0.7991 (mm-30) cc_final: 0.7672 (mm-30) REVERT: A 546 ASN cc_start: 0.8502 (t0) cc_final: 0.8194 (t0) REVERT: A 675 MET cc_start: 0.6394 (tmm) cc_final: 0.6148 (tmm) REVERT: A 886 ASN cc_start: 0.8522 (t0) cc_final: 0.7921 (t0) REVERT: B 237 GLN cc_start: 0.8006 (mp10) cc_final: 0.7590 (mp10) REVERT: B 323 ARG cc_start: 0.7448 (ptt-90) cc_final: 0.7153 (ptt90) REVERT: B 807 LYS cc_start: 0.7235 (mttt) cc_final: 0.6658 (mtpp) REVERT: C 386 GLU cc_start: 0.6992 (mm-30) cc_final: 0.6704 (tp30) REVERT: C 403 ILE cc_start: 0.8283 (mm) cc_final: 0.7915 (mm) outliers start: 43 outliers final: 35 residues processed: 304 average time/residue: 0.1346 time to fit residues: 62.1554 Evaluate side-chains 314 residues out of total 1890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 279 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 462 MET Chi-restraints excluded: chain A residue 479 MET Chi-restraints excluded: chain A residue 611 THR Chi-restraints excluded: chain A residue 679 ASN Chi-restraints excluded: chain A residue 684 PHE Chi-restraints excluded: chain A residue 718 ILE Chi-restraints excluded: chain A residue 842 THR Chi-restraints excluded: chain A residue 891 VAL Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 600 LEU Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain B residue 679 ASN Chi-restraints excluded: chain B residue 684 PHE Chi-restraints excluded: chain B residue 694 THR Chi-restraints excluded: chain B residue 719 SER Chi-restraints excluded: chain B residue 726 THR Chi-restraints excluded: chain B residue 842 THR Chi-restraints excluded: chain C residue 443 VAL Chi-restraints excluded: chain C residue 455 VAL Chi-restraints excluded: chain C residue 490 HIS Chi-restraints excluded: chain C residue 600 LEU Chi-restraints excluded: chain C residue 611 THR Chi-restraints excluded: chain C residue 679 ASN Chi-restraints excluded: chain C residue 684 PHE Chi-restraints excluded: chain C residue 694 THR Chi-restraints excluded: chain C residue 719 SER Chi-restraints excluded: chain C residue 726 THR Chi-restraints excluded: chain C residue 842 THR Chi-restraints excluded: chain C residue 891 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 66 optimal weight: 7.9990 chunk 167 optimal weight: 0.6980 chunk 4 optimal weight: 1.9990 chunk 144 optimal weight: 5.9990 chunk 102 optimal weight: 0.7980 chunk 193 optimal weight: 4.9990 chunk 189 optimal weight: 0.6980 chunk 164 optimal weight: 0.5980 chunk 95 optimal weight: 0.6980 chunk 47 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 513 HIS ** A 898 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 898 HIS ** C 898 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.189390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.140981 restraints weight = 21253.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.135921 restraints weight = 18310.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.138003 restraints weight = 19327.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.138518 restraints weight = 10687.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.140206 restraints weight = 9663.808| |-----------------------------------------------------------------------------| r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 moved from start: 0.2449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 18192 Z= 0.127 Angle : 0.609 14.343 24735 Z= 0.291 Chirality : 0.041 0.200 2727 Planarity : 0.004 0.076 3081 Dihedral : 4.133 29.789 2616 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.01 % Allowed : 15.29 % Favored : 82.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.79 (0.18), residues: 2163 helix: 1.78 (0.16), residues: 1158 sheet: -0.48 (0.38), residues: 165 loop : -1.08 (0.20), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 323 TYR 0.022 0.001 TYR C 608 PHE 0.011 0.001 PHE B 397 TRP 0.017 0.001 TRP A 784 HIS 0.004 0.001 HIS B 514 Details of bonding type rmsd covalent geometry : bond 0.00305 (18186) covalent geometry : angle 0.60565 (24717) hydrogen bonds : bond 0.03308 ( 854) hydrogen bonds : angle 3.70541 ( 2535) link_BETA1-4 : bond 0.00392 ( 6) link_BETA1-4 : angle 2.51102 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 1890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 284 time to evaluate : 0.648 Fit side-chains REVERT: A 237 GLN cc_start: 0.7924 (mp10) cc_final: 0.7596 (pm20) REVERT: A 241 ARG cc_start: 0.7275 (ttp-110) cc_final: 0.6788 (ptp-170) REVERT: A 360 MET cc_start: 0.8384 (ttp) cc_final: 0.8108 (ttp) REVERT: A 389 GLU cc_start: 0.7965 (mm-30) cc_final: 0.7654 (mm-30) REVERT: A 546 ASN cc_start: 0.8497 (t0) cc_final: 0.8172 (t0) REVERT: A 675 MET cc_start: 0.6304 (tmm) cc_final: 0.6028 (tmm) REVERT: A 784 TRP cc_start: 0.8100 (m-10) cc_final: 0.7765 (m-10) REVERT: A 886 ASN cc_start: 0.8521 (t0) cc_final: 0.7920 (t0) REVERT: B 237 GLN cc_start: 0.7964 (mp10) cc_final: 0.7580 (pm20) REVERT: B 323 ARG cc_start: 0.7437 (ptt-90) cc_final: 0.7161 (ptt90) REVERT: B 389 GLU cc_start: 0.7895 (mm-30) cc_final: 0.7503 (mm-30) REVERT: B 807 LYS cc_start: 0.7207 (mttt) cc_final: 0.6633 (mtpp) REVERT: C 386 GLU cc_start: 0.6972 (mm-30) cc_final: 0.6687 (tp30) REVERT: C 403 ILE cc_start: 0.8289 (mm) cc_final: 0.7928 (mm) outliers start: 38 outliers final: 35 residues processed: 303 average time/residue: 0.1374 time to fit residues: 63.0356 Evaluate side-chains 313 residues out of total 1890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 278 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 479 MET Chi-restraints excluded: chain A residue 611 THR Chi-restraints excluded: chain A residue 679 ASN Chi-restraints excluded: chain A residue 684 PHE Chi-restraints excluded: chain A residue 718 ILE Chi-restraints excluded: chain A residue 726 THR Chi-restraints excluded: chain A residue 842 THR Chi-restraints excluded: chain A residue 891 VAL Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 600 LEU Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain B residue 679 ASN Chi-restraints excluded: chain B residue 684 PHE Chi-restraints excluded: chain B residue 694 THR Chi-restraints excluded: chain B residue 719 SER Chi-restraints excluded: chain B residue 726 THR Chi-restraints excluded: chain B residue 842 THR Chi-restraints excluded: chain C residue 443 VAL Chi-restraints excluded: chain C residue 455 VAL Chi-restraints excluded: chain C residue 490 HIS Chi-restraints excluded: chain C residue 600 LEU Chi-restraints excluded: chain C residue 611 THR Chi-restraints excluded: chain C residue 679 ASN Chi-restraints excluded: chain C residue 684 PHE Chi-restraints excluded: chain C residue 694 THR Chi-restraints excluded: chain C residue 719 SER Chi-restraints excluded: chain C residue 726 THR Chi-restraints excluded: chain C residue 842 THR Chi-restraints excluded: chain C residue 891 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 127 optimal weight: 3.9990 chunk 176 optimal weight: 0.5980 chunk 170 optimal weight: 0.9990 chunk 194 optimal weight: 0.8980 chunk 17 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 191 optimal weight: 0.7980 chunk 184 optimal weight: 1.9990 chunk 25 optimal weight: 0.0970 chunk 85 optimal weight: 0.8980 chunk 89 optimal weight: 0.8980 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 513 HIS ** A 898 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 898 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.189683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.140884 restraints weight = 21453.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.134855 restraints weight = 19149.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.137758 restraints weight = 19746.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.137770 restraints weight = 11667.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.141130 restraints weight = 10661.700| |-----------------------------------------------------------------------------| r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.2521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18192 Z= 0.123 Angle : 0.606 15.104 24735 Z= 0.290 Chirality : 0.042 0.256 2727 Planarity : 0.004 0.072 3081 Dihedral : 3.972 18.477 2616 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.12 % Allowed : 15.45 % Favored : 82.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.83 (0.18), residues: 2163 helix: 1.81 (0.16), residues: 1158 sheet: -0.44 (0.38), residues: 165 loop : -1.05 (0.20), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 323 TYR 0.015 0.001 TYR B 758 PHE 0.011 0.001 PHE B 397 TRP 0.019 0.001 TRP B 784 HIS 0.004 0.001 HIS B 514 Details of bonding type rmsd covalent geometry : bond 0.00295 (18186) covalent geometry : angle 0.60281 (24717) hydrogen bonds : bond 0.03247 ( 854) hydrogen bonds : angle 3.69683 ( 2535) link_BETA1-4 : bond 0.00375 ( 6) link_BETA1-4 : angle 2.36039 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2883.41 seconds wall clock time: 50 minutes 42.95 seconds (3042.95 seconds total)