Starting phenix.real_space_refine on Sun Jun 15 20:58:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7d5k_30583/06_2025/7d5k_30583.cif Found real_map, /net/cci-nas-00/data/ceres_data/7d5k_30583/06_2025/7d5k_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7d5k_30583/06_2025/7d5k_30583.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7d5k_30583/06_2025/7d5k_30583.map" model { file = "/net/cci-nas-00/data/ceres_data/7d5k_30583/06_2025/7d5k_30583.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7d5k_30583/06_2025/7d5k_30583.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 11.24, per 1000 atoms: 0.64 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: 6.58 Conformation dependent library (CDL) restraints added in 4.4 seconds 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: 2.12 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: 9.15 Time building geometry restraints manager: 6.44 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: 0.12 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: 49.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.780 Check model and map are aligned: 0.130 Set scattering table: 0.180 Process input model: 53.110 Find NCS groups from input model: 0.950 Set up NCS constraints: 0.170 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: 0.020 Load rotamer database and sin/cos tables:4.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 109.020 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.024 0.001 TRP C 800 HIS 0.003 0.001 HIS A 986 PHE 0.034 0.001 PHE B 306 TYR 0.020 0.002 TYR B 758 ARG 0.006 0.001 ARG C 795 Details of bonding type rmsd link_BETA1-4 : bond 0.00218 ( 6) link_BETA1-4 : angle 2.12977 ( 18) hydrogen bonds : bond 0.12407 ( 854) hydrogen bonds : angle 5.06698 ( 2535) covalent geometry : bond 0.00328 (18186) covalent geometry : angle 0.69063 (24717) *********************** 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 : 2.329 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: 0.7563 (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: 0.7808 (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: 0.4521 time to fit residues: 226.2205 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 : 3.949 ------------------------------------------------------------------------------- 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 182 optimal weight: 1.9990 chunk 163 optimal weight: 0.7980 chunk 90 optimal weight: 0.6980 chunk 55 optimal weight: 3.9990 chunk 110 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 169 optimal weight: 2.9990 chunk 65 optimal weight: 10.0000 chunk 102 optimal weight: 1.9990 chunk 126 optimal weight: 0.6980 chunk 196 optimal weight: 0.0470 overall best weight: 0.8480 ------------------------------------------------------------------------------- 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 = 0.3932 r_free = 0.3932 target = 0.189753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.140825 restraints weight = 21155.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.139903 restraints weight = 17530.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.140741 restraints weight = 21256.086| |-----------------------------------------------------------------------------| r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7470 moved from start: 0.1133 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 : 0.638 7.693 24735 Z= 0.315 Chirality : 0.044 0.190 2727 Planarity : 0.004 0.041 3081 Dihedral : 9.282 95.464 2625 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 1.80 % Allowed : 6.93 % Favored : 91.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.18), residues: 2163 helix: 1.05 (0.15), residues: 1173 sheet: -1.19 (0.37), residues: 162 loop : -1.22 (0.20), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 800 HIS 0.005 0.001 HIS B 514 PHE 0.027 0.001 PHE B 306 TYR 0.021 0.002 TYR C 758 ARG 0.006 0.001 ARG A 795 Details of bonding type rmsd link_BETA1-4 : bond 0.00222 ( 6) link_BETA1-4 : angle 2.88672 ( 18) hydrogen bonds : bond 0.04303 ( 854) hydrogen bonds : angle 4.26206 ( 2535) covalent geometry : bond 0.00354 (18186) covalent geometry : angle 0.63370 (24717) *********************** 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 357 residues out of total 1890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 323 time to evaluate : 2.374 Fit side-chains REVERT: A 237 GLN cc_start: 0.7927 (mp10) cc_final: 0.7557 (mp10) REVERT: A 360 MET cc_start: 0.8390 (ttp) cc_final: 0.8091 (ttp) REVERT: A 389 GLU cc_start: 0.8128 (mm-30) cc_final: 0.7589 (mm-30) REVERT: A 434 MET cc_start: 0.8467 (tpp) cc_final: 0.8200 (tpp) REVERT: A 493 GLU cc_start: 0.7950 (mm-30) cc_final: 0.7715 (mm-30) REVERT: A 527 SER cc_start: 0.8888 (m) cc_final: 0.8673 (m) REVERT: A 553 GLU cc_start: 0.7646 (tt0) cc_final: 0.7440 (tt0) REVERT: A 555 MET cc_start: 0.8942 (mmt) cc_final: 0.8685 (mmt) REVERT: A 886 ASN cc_start: 0.8329 (t0) cc_final: 0.7753 (t0) REVERT: B 389 GLU cc_start: 0.8040 (mm-30) cc_final: 0.7594 (mm-30) REVERT: B 527 SER cc_start: 0.9005 (m) cc_final: 0.8763 (m) REVERT: B 555 MET cc_start: 0.8982 (mmt) cc_final: 0.8669 (mmm) REVERT: B 807 LYS cc_start: 0.7265 (mttt) cc_final: 0.6664 (mtpp) REVERT: C 237 GLN cc_start: 0.8112 (mp10) cc_final: 0.7704 (mp10) REVERT: C 403 ILE cc_start: 0.8175 (mm) cc_final: 0.7826 (mm) REVERT: C 474 LYS cc_start: 0.7841 (mttp) cc_final: 0.7609 (mmtp) REVERT: C 783 ARG cc_start: 0.7227 (mtp-110) cc_final: 0.6998 (mtp-110) REVERT: C 795 ARG cc_start: 0.7120 (ptt-90) cc_final: 0.6761 (ptt-90) REVERT: C 908 LYS cc_start: 0.7867 (ttpt) cc_final: 0.7554 (tttm) outliers start: 34 outliers final: 27 residues processed: 331 average time/residue: 0.4629 time to fit residues: 231.7194 Evaluate side-chains 306 residues out of total 1890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 279 time to evaluate : 1.985 ------------------------------------------------------------------------------- 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 490 HIS 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 719 SER Chi-restraints excluded: chain A residue 726 THR Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 462 MET Chi-restraints excluded: chain B residue 490 HIS 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 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 187 optimal weight: 0.9980 chunk 141 optimal weight: 10.0000 chunk 137 optimal weight: 4.9990 chunk 79 optimal weight: 2.9990 chunk 40 optimal weight: 0.6980 chunk 84 optimal weight: 0.5980 chunk 18 optimal weight: 0.5980 chunk 92 optimal weight: 0.6980 chunk 81 optimal weight: 0.8980 chunk 194 optimal weight: 3.9990 chunk 118 optimal weight: 1.9990 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 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 = 0.3931 r_free = 0.3931 target = 0.189905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.141309 restraints weight = 21403.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.137094 restraints weight = 17285.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.138365 restraints weight = 22726.622| |-----------------------------------------------------------------------------| r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7500 moved from start: 0.1452 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= 0.132 Angle : 0.603 7.885 24735 Z= 0.293 Chirality : 0.042 0.176 2727 Planarity : 0.004 0.037 3081 Dihedral : 6.381 48.690 2616 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 1.43 % Allowed : 10.79 % Favored : 87.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.18), residues: 2163 helix: 1.25 (0.16), residues: 1176 sheet: -0.88 (0.38), residues: 165 loop : -1.20 (0.20), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 800 HIS 0.004 0.001 HIS B 514 PHE 0.019 0.001 PHE A 306 TYR 0.016 0.001 TYR C 758 ARG 0.006 0.000 ARG A 795 Details of bonding type rmsd link_BETA1-4 : bond 0.00289 ( 6) link_BETA1-4 : angle 3.23216 ( 18) hydrogen bonds : bond 0.03896 ( 854) hydrogen bonds : angle 4.03117 ( 2535) covalent geometry : bond 0.00308 (18186) covalent geometry : angle 0.59733 (24717) *********************** 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 317 residues out of total 1890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 290 time to evaluate : 3.205 Fit side-chains REVERT: A 237 GLN cc_start: 0.7941 (mp10) cc_final: 0.7355 (mp10) REVERT: A 255 MET cc_start: 0.7460 (mtm) cc_final: 0.7258 (mtm) REVERT: A 360 MET cc_start: 0.8435 (ttp) cc_final: 0.8159 (ttp) REVERT: A 373 ASP cc_start: 0.8419 (t0) cc_final: 0.8151 (t0) REVERT: A 389 GLU cc_start: 0.8105 (mm-30) cc_final: 0.7648 (mm-30) REVERT: A 546 ASN cc_start: 0.8508 (t0) cc_final: 0.8199 (t0) REVERT: A 553 GLU cc_start: 0.7721 (tt0) cc_final: 0.7453 (mt-10) REVERT: A 886 ASN cc_start: 0.8371 (t0) cc_final: 0.7794 (t0) REVERT: B 237 GLN cc_start: 0.7977 (mp10) cc_final: 0.7549 (mp10) REVERT: B 389 GLU cc_start: 0.8001 (mm-30) cc_final: 0.7534 (mm-30) REVERT: B 807 LYS cc_start: 0.7193 (mttt) cc_final: 0.6564 (mtpp) REVERT: C 237 GLN cc_start: 0.8064 (mp10) cc_final: 0.7445 (mp10) REVERT: C 403 ILE cc_start: 0.8193 (mm) cc_final: 0.7824 (mm) REVERT: C 474 LYS cc_start: 0.7811 (mttp) cc_final: 0.7582 (mmtp) REVERT: C 786 LEU cc_start: 0.8347 (tp) cc_final: 0.8068 (tp) REVERT: C 795 ARG cc_start: 0.7148 (ptt-90) cc_final: 0.6890 (ptt-90) REVERT: C 847 MET cc_start: 0.8977 (pmm) cc_final: 0.8755 (pmm) REVERT: C 908 LYS cc_start: 0.8274 (ttpt) cc_final: 0.7894 (tttm) outliers start: 27 outliers final: 23 residues processed: 299 average time/residue: 0.5062 time to fit residues: 232.9609 Evaluate side-chains 294 residues out of total 1890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 271 time to evaluate : 4.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 421 ASP Chi-restraints excluded: chain A residue 443 VAL 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 719 SER 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 C residue 245 ILE Chi-restraints excluded: chain C residue 443 VAL 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 719 SER Chi-restraints excluded: chain C residue 726 THR 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 99 optimal weight: 0.5980 chunk 192 optimal weight: 2.9990 chunk 5 optimal weight: 0.6980 chunk 167 optimal weight: 0.2980 chunk 6 optimal weight: 20.0000 chunk 200 optimal weight: 9.9990 chunk 26 optimal weight: 0.7980 chunk 4 optimal weight: 0.6980 chunk 145 optimal weight: 7.9990 chunk 142 optimal weight: 0.0770 chunk 183 optimal weight: 1.9990 overall best weight: 0.4738 ------------------------------------------------------------------------------- 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 = 0.3940 r_free = 0.3940 target = 0.190740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.141954 restraints weight = 21385.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.137395 restraints weight = 16607.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.138704 restraints weight = 22059.223| |-----------------------------------------------------------------------------| r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 moved from start: 0.1701 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= 0.115 Angle : 0.578 7.740 24735 Z= 0.279 Chirality : 0.041 0.182 2727 Planarity : 0.004 0.077 3081 Dihedral : 5.474 46.916 2616 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 1.80 % Allowed : 12.01 % Favored : 86.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.18), residues: 2163 helix: 1.47 (0.16), residues: 1158 sheet: -0.60 (0.40), residues: 165 loop : -1.13 (0.20), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 800 HIS 0.003 0.001 HIS B 514 PHE 0.014 0.001 PHE B 306 TYR 0.017 0.001 TYR A 621 ARG 0.007 0.000 ARG A 795 Details of bonding type rmsd link_BETA1-4 : bond 0.00448 ( 6) link_BETA1-4 : angle 3.19729 ( 18) hydrogen bonds : bond 0.03509 ( 854) hydrogen bonds : angle 3.86210 ( 2535) covalent geometry : bond 0.00264 (18186) covalent geometry : angle 0.57168 (24717) *********************** 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 347 residues out of total 1890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 313 time to evaluate : 2.564 Fit side-chains REVERT: A 237 GLN cc_start: 0.7941 (mp10) cc_final: 0.7374 (mp10) REVERT: A 360 MET cc_start: 0.8387 (ttp) cc_final: 0.8089 (ttp) REVERT: A 373 ASP cc_start: 0.8330 (t0) cc_final: 0.7992 (t0) REVERT: A 389 GLU cc_start: 0.8047 (mm-30) cc_final: 0.7688 (mm-30) REVERT: A 546 ASN cc_start: 0.8550 (t0) cc_final: 0.8221 (t0) REVERT: A 675 MET cc_start: 0.6467 (tmm) cc_final: 0.6164 (tmm) REVERT: A 886 ASN cc_start: 0.8401 (t0) cc_final: 0.7734 (t0) REVERT: B 237 GLN cc_start: 0.8044 (mp10) cc_final: 0.7535 (mp10) REVERT: B 389 GLU cc_start: 0.7964 (mm-30) cc_final: 0.7626 (mm-30) REVERT: B 807 LYS cc_start: 0.7235 (mttt) cc_final: 0.6627 (mtpp) REVERT: C 237 GLN cc_start: 0.8006 (mp10) cc_final: 0.7552 (pm20) REVERT: C 373 ASP cc_start: 0.8332 (t0) cc_final: 0.8115 (t0) REVERT: C 403 ILE cc_start: 0.8052 (mm) cc_final: 0.7658 (mm) REVERT: C 474 LYS cc_start: 0.7821 (mttp) cc_final: 0.7616 (mmtp) REVERT: C 752 ARG cc_start: 0.7277 (mtt180) cc_final: 0.7018 (mtt180) REVERT: C 908 LYS cc_start: 0.8305 (ttpt) cc_final: 0.7927 (tttm) outliers start: 34 outliers final: 24 residues processed: 326 average time/residue: 0.4907 time to fit residues: 248.2766 Evaluate side-chains 306 residues out of total 1890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 282 time to evaluate : 2.921 ------------------------------------------------------------------------------- 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 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 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 726 THR Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain C residue 443 VAL 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 715 ILE Chi-restraints excluded: chain C residue 773 ASN 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 138 optimal weight: 4.9990 chunk 204 optimal weight: 0.1980 chunk 84 optimal weight: 0.9980 chunk 105 optimal weight: 2.9990 chunk 68 optimal weight: 8.9990 chunk 203 optimal weight: 0.9990 chunk 180 optimal weight: 2.9990 chunk 116 optimal weight: 0.9980 chunk 40 optimal weight: 0.9980 chunk 165 optimal weight: 0.7980 chunk 3 optimal weight: 3.9990 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 = 0.3922 r_free = 0.3922 target = 0.188860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.139766 restraints weight = 21635.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.135438 restraints weight = 16936.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.136796 restraints weight = 21857.365| |-----------------------------------------------------------------------------| r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.1902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 18192 Z= 0.135 Angle : 0.600 8.937 24735 Z= 0.289 Chirality : 0.042 0.185 2727 Planarity : 0.004 0.045 3081 Dihedral : 5.289 45.871 2616 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 2.43 % Allowed : 12.75 % Favored : 84.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.18), residues: 2163 helix: 1.53 (0.16), residues: 1161 sheet: -0.59 (0.40), residues: 165 loop : -1.10 (0.20), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 800 HIS 0.005 0.001 HIS A 514 PHE 0.012 0.001 PHE B 397 TYR 0.015 0.001 TYR A 758 ARG 0.006 0.000 ARG B 565 Details of bonding type rmsd link_BETA1-4 : bond 0.00530 ( 6) link_BETA1-4 : angle 3.29175 ( 18) hydrogen bonds : bond 0.03609 ( 854) hydrogen bonds : angle 3.84062 ( 2535) covalent geometry : bond 0.00322 (18186) covalent geometry : angle 0.59331 (24717) *********************** 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 341 residues out of total 1890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 295 time to evaluate : 2.063 Fit side-chains REVERT: A 237 GLN cc_start: 0.7970 (mp10) cc_final: 0.7465 (mp10) REVERT: A 360 MET cc_start: 0.8447 (ttp) cc_final: 0.8146 (ttp) REVERT: A 373 ASP cc_start: 0.8372 (t0) cc_final: 0.7968 (t0) REVERT: A 389 GLU cc_start: 0.8054 (mm-30) cc_final: 0.7660 (mm-30) REVERT: A 546 ASN cc_start: 0.8553 (t0) cc_final: 0.8226 (t0) REVERT: A 886 ASN cc_start: 0.8619 (t0) cc_final: 0.8064 (t0) REVERT: B 237 GLN cc_start: 0.8091 (mp10) cc_final: 0.7577 (mp10) REVERT: B 334 ASP cc_start: 0.8310 (m-30) cc_final: 0.8089 (m-30) REVERT: B 389 GLU cc_start: 0.7980 (mm-30) cc_final: 0.7603 (mm-30) REVERT: B 807 LYS cc_start: 0.7237 (mttt) cc_final: 0.6638 (mtpp) REVERT: C 237 GLN cc_start: 0.8014 (mp10) cc_final: 0.7686 (pm20) REVERT: C 373 ASP cc_start: 0.8345 (t0) cc_final: 0.8037 (t0) REVERT: C 389 GLU cc_start: 0.8241 (mm-30) cc_final: 0.7986 (mm-30) REVERT: C 403 ILE cc_start: 0.8223 (mm) cc_final: 0.7850 (mm) REVERT: C 474 LYS cc_start: 0.7817 (mttp) cc_final: 0.7606 (mmtp) REVERT: C 752 ARG cc_start: 0.7310 (mtt180) cc_final: 0.7067 (mtt180) REVERT: C 908 LYS cc_start: 0.8305 (ttpt) cc_final: 0.7912 (tttm) outliers start: 46 outliers final: 36 residues processed: 317 average time/residue: 0.3121 time to fit residues: 149.2198 Evaluate side-chains 320 residues out of total 1890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 284 time to evaluate : 1.986 ------------------------------------------------------------------------------- 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 567 VAL Chi-restraints excluded: chain A residue 603 ILE 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 726 THR Chi-restraints excluded: chain A residue 891 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 773 ASN 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 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 726 THR 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 147 optimal weight: 0.6980 chunk 81 optimal weight: 0.9980 chunk 22 optimal weight: 3.9990 chunk 136 optimal weight: 4.9990 chunk 153 optimal weight: 0.2980 chunk 212 optimal weight: 6.9990 chunk 43 optimal weight: 0.7980 chunk 213 optimal weight: 8.9990 chunk 133 optimal weight: 1.9990 chunk 139 optimal weight: 20.0000 chunk 14 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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 = 0.3913 r_free = 0.3913 target = 0.187807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.137865 restraints weight = 21538.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.134777 restraints weight = 16658.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.136142 restraints weight = 20284.065| |-----------------------------------------------------------------------------| r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.2084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 18192 Z= 0.147 Angle : 0.606 8.056 24735 Z= 0.293 Chirality : 0.042 0.197 2727 Planarity : 0.004 0.065 3081 Dihedral : 5.239 58.017 2616 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 2.65 % Allowed : 13.23 % Favored : 84.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.18), residues: 2163 helix: 1.58 (0.16), residues: 1161 sheet: -0.60 (0.39), residues: 165 loop : -1.13 (0.20), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 800 HIS 0.004 0.001 HIS A 514 PHE 0.011 0.001 PHE B 397 TYR 0.021 0.002 TYR A 621 ARG 0.007 0.000 ARG B 565 Details of bonding type rmsd link_BETA1-4 : bond 0.00526 ( 6) link_BETA1-4 : angle 3.36276 ( 18) hydrogen bonds : bond 0.03691 ( 854) hydrogen bonds : angle 3.83573 ( 2535) covalent geometry : bond 0.00354 (18186) covalent geometry : angle 0.59947 (24717) *********************** 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 355 residues out of total 1890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 305 time to evaluate : 1.864 Fit side-chains REVERT: A 237 GLN cc_start: 0.7997 (mp10) cc_final: 0.7480 (mp10) REVERT: A 360 MET cc_start: 0.8461 (ttp) cc_final: 0.8220 (ttp) REVERT: A 389 GLU cc_start: 0.8041 (mm-30) cc_final: 0.7653 (mm-30) REVERT: A 546 ASN cc_start: 0.8518 (t0) cc_final: 0.8185 (t0) REVERT: A 675 MET cc_start: 0.6626 (tmm) cc_final: 0.6402 (tmm) REVERT: A 784 TRP cc_start: 0.7927 (m-10) cc_final: 0.7466 (m-10) REVERT: A 886 ASN cc_start: 0.8667 (t0) cc_final: 0.7987 (t0) REVERT: B 237 GLN cc_start: 0.8096 (mp10) cc_final: 0.7622 (mp10) REVERT: B 334 ASP cc_start: 0.8290 (m-30) cc_final: 0.8088 (m-30) REVERT: B 373 ASP cc_start: 0.8591 (t0) cc_final: 0.8184 (t70) REVERT: B 389 GLU cc_start: 0.7976 (mm-30) cc_final: 0.7619 (mm-30) REVERT: B 807 LYS cc_start: 0.7307 (mttt) cc_final: 0.6677 (mtpp) REVERT: C 237 GLN cc_start: 0.8066 (mp10) cc_final: 0.7736 (pm20) REVERT: C 373 ASP cc_start: 0.8354 (t0) cc_final: 0.7991 (t0) REVERT: C 389 GLU cc_start: 0.8259 (mm-30) cc_final: 0.8035 (mm-30) REVERT: C 403 ILE cc_start: 0.8213 (mm) cc_final: 0.7852 (mm) REVERT: C 474 LYS cc_start: 0.7817 (mttp) cc_final: 0.7602 (mmtp) REVERT: C 752 ARG cc_start: 0.7352 (mtt180) cc_final: 0.7141 (mtt180) REVERT: C 847 MET cc_start: 0.8927 (pmm) cc_final: 0.8711 (pmm) REVERT: C 908 LYS cc_start: 0.8349 (ttpt) cc_final: 0.7995 (tttm) outliers start: 50 outliers final: 38 residues processed: 332 average time/residue: 0.3165 time to fit residues: 158.0585 Evaluate side-chains 325 residues out of total 1890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 287 time to evaluate : 2.133 ------------------------------------------------------------------------------- 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 479 MET Chi-restraints excluded: chain A residue 567 VAL 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 726 THR Chi-restraints excluded: chain A residue 891 VAL Chi-restraints excluded: chain B residue 245 ILE 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 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 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 773 ASN 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 180 optimal weight: 0.8980 chunk 183 optimal weight: 0.7980 chunk 181 optimal weight: 2.9990 chunk 1 optimal weight: 5.9990 chunk 18 optimal weight: 2.9990 chunk 204 optimal weight: 7.9990 chunk 146 optimal weight: 0.7980 chunk 144 optimal weight: 5.9990 chunk 160 optimal weight: 1.9990 chunk 124 optimal weight: 0.0470 chunk 166 optimal weight: 0.7980 overall best weight: 0.6678 ------------------------------------------------------------------------------- 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 = 0.3922 r_free = 0.3922 target = 0.188765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.139397 restraints weight = 21335.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.135420 restraints weight = 16505.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.136893 restraints weight = 20851.679| |-----------------------------------------------------------------------------| r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.2162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 18192 Z= 0.124 Angle : 0.594 10.343 24735 Z= 0.286 Chirality : 0.041 0.196 2727 Planarity : 0.004 0.045 3081 Dihedral : 4.903 47.355 2616 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 2.33 % Allowed : 14.18 % Favored : 83.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.18), residues: 2163 helix: 1.62 (0.16), residues: 1161 sheet: -0.56 (0.39), residues: 165 loop : -1.10 (0.20), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 800 HIS 0.003 0.001 HIS A 514 PHE 0.011 0.001 PHE B 397 TYR 0.019 0.001 TYR A 621 ARG 0.008 0.000 ARG A 323 Details of bonding type rmsd link_BETA1-4 : bond 0.00508 ( 6) link_BETA1-4 : angle 3.05763 ( 18) hydrogen bonds : bond 0.03473 ( 854) hydrogen bonds : angle 3.77158 ( 2535) covalent geometry : bond 0.00295 (18186) covalent geometry : angle 0.58821 (24717) *********************** 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 340 residues out of total 1890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 296 time to evaluate : 2.801 Fit side-chains revert: symmetry clash REVERT: A 237 GLN cc_start: 0.7980 (mp10) cc_final: 0.7582 (pm20) REVERT: A 360 MET cc_start: 0.8434 (ttp) cc_final: 0.8149 (ttp) REVERT: A 373 ASP cc_start: 0.8622 (t0) cc_final: 0.8179 (t0) REVERT: A 389 GLU cc_start: 0.8035 (mm-30) cc_final: 0.7715 (mm-30) REVERT: A 546 ASN cc_start: 0.8520 (t0) cc_final: 0.8186 (t0) REVERT: A 886 ASN cc_start: 0.8663 (t0) cc_final: 0.7980 (t0) REVERT: B 237 GLN cc_start: 0.8083 (mp10) cc_final: 0.7619 (mp10) REVERT: B 323 ARG cc_start: 0.7413 (ptt-90) cc_final: 0.7073 (ptt90) REVERT: B 389 GLU cc_start: 0.7959 (mm-30) cc_final: 0.7597 (mm-30) REVERT: B 511 PHE cc_start: 0.7603 (m-80) cc_final: 0.7387 (m-80) REVERT: B 807 LYS cc_start: 0.7245 (mttt) cc_final: 0.6651 (mtpp) REVERT: B 908 LYS cc_start: 0.7671 (ttpt) cc_final: 0.7376 (tttt) REVERT: C 237 GLN cc_start: 0.8061 (mp10) cc_final: 0.7757 (pm20) REVERT: C 389 GLU cc_start: 0.8244 (mm-30) cc_final: 0.8019 (mm-30) REVERT: C 403 ILE cc_start: 0.8170 (mm) cc_final: 0.7798 (mm) REVERT: C 474 LYS cc_start: 0.7792 (mttp) cc_final: 0.7577 (mmtp) REVERT: C 752 ARG cc_start: 0.7330 (mtt180) cc_final: 0.7107 (mtt180) REVERT: C 847 MET cc_start: 0.8939 (pmm) cc_final: 0.8728 (pmm) REVERT: C 908 LYS cc_start: 0.8346 (ttpt) cc_final: 0.7971 (tttm) outliers start: 44 outliers final: 36 residues processed: 314 average time/residue: 0.3635 time to fit residues: 172.8304 Evaluate side-chains 320 residues out of total 1890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 284 time to evaluate : 2.478 ------------------------------------------------------------------------------- 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 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 718 ILE Chi-restraints excluded: chain A residue 726 THR Chi-restraints excluded: chain A residue 891 VAL Chi-restraints excluded: chain B residue 242 LYS 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 718 ILE 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 360 MET Chi-restraints excluded: chain C residue 417 ASP Chi-restraints excluded: chain C residue 443 VAL Chi-restraints excluded: chain C residue 455 VAL 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 773 ASN 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 111 optimal weight: 0.7980 chunk 145 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 21 optimal weight: 0.0270 chunk 196 optimal weight: 4.9990 chunk 59 optimal weight: 1.9990 chunk 180 optimal weight: 3.9990 chunk 81 optimal weight: 0.9990 chunk 176 optimal weight: 0.9990 chunk 119 optimal weight: 0.8980 chunk 30 optimal weight: 0.5980 overall best weight: 0.6640 ------------------------------------------------------------------------------- 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 = 0.3925 r_free = 0.3925 target = 0.189039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.139448 restraints weight = 21373.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.135763 restraints weight = 16522.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.137327 restraints weight = 20105.053| |-----------------------------------------------------------------------------| r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.2304 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= 0.124 Angle : 0.591 12.040 24735 Z= 0.285 Chirality : 0.041 0.200 2727 Planarity : 0.004 0.034 3081 Dihedral : 4.563 54.062 2616 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.28 % Allowed : 14.55 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.18), residues: 2163 helix: 1.72 (0.16), residues: 1158 sheet: -0.55 (0.39), residues: 165 loop : -1.09 (0.20), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 784 HIS 0.004 0.001 HIS B 514 PHE 0.011 0.001 PHE B 397 TYR 0.021 0.001 TYR C 608 ARG 0.009 0.000 ARG C 323 Details of bonding type rmsd link_BETA1-4 : bond 0.00453 ( 6) link_BETA1-4 : angle 2.83925 ( 18) hydrogen bonds : bond 0.03372 ( 854) hydrogen bonds : angle 3.72093 ( 2535) covalent geometry : bond 0.00294 (18186) covalent geometry : angle 0.58596 (24717) *********************** 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 332 residues out of total 1890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 289 time to evaluate : 2.019 Fit side-chains revert: symmetry clash REVERT: A 237 GLN cc_start: 0.7970 (mp10) cc_final: 0.7593 (pm20) REVERT: A 360 MET cc_start: 0.8397 (ttp) cc_final: 0.8128 (ttp) REVERT: A 389 GLU cc_start: 0.8005 (mm-30) cc_final: 0.7695 (mm-30) REVERT: A 546 ASN cc_start: 0.8540 (t0) cc_final: 0.8218 (t0) REVERT: A 757 ILE cc_start: 0.8946 (tt) cc_final: 0.8542 (mt) REVERT: A 784 TRP cc_start: 0.8042 (m-10) cc_final: 0.7641 (m-10) REVERT: A 886 ASN cc_start: 0.8627 (t0) cc_final: 0.8009 (t0) REVERT: B 237 GLN cc_start: 0.8051 (mp10) cc_final: 0.7600 (mp10) REVERT: B 255 MET cc_start: 0.7122 (mtm) cc_final: 0.6918 (mtm) REVERT: B 323 ARG cc_start: 0.7461 (ptt-90) cc_final: 0.7164 (ptt90) REVERT: B 807 LYS cc_start: 0.7259 (mttt) cc_final: 0.6664 (mtpp) REVERT: C 237 GLN cc_start: 0.7887 (mp10) cc_final: 0.7642 (pm20) REVERT: C 386 GLU cc_start: 0.7012 (mm-30) cc_final: 0.6759 (tp30) REVERT: C 403 ILE cc_start: 0.8129 (mm) cc_final: 0.7742 (mm) REVERT: C 474 LYS cc_start: 0.7800 (mttp) cc_final: 0.7584 (mmtp) REVERT: C 908 LYS cc_start: 0.8349 (ttpt) cc_final: 0.7965 (tttm) outliers start: 43 outliers final: 38 residues processed: 312 average time/residue: 0.3084 time to fit residues: 144.5695 Evaluate side-chains 320 residues out of total 1890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 282 time to evaluate : 1.974 ------------------------------------------------------------------------------- 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 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 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 242 LYS 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 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 C residue 360 MET Chi-restraints excluded: chain C residue 417 ASP 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 715 ILE 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 891 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 50 optimal weight: 0.8980 chunk 86 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 190 optimal weight: 0.9980 chunk 65 optimal weight: 6.9990 chunk 24 optimal weight: 0.9990 chunk 102 optimal weight: 0.7980 chunk 141 optimal weight: 4.9990 chunk 158 optimal weight: 0.8980 chunk 175 optimal weight: 1.9990 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 = 0.3926 r_free = 0.3926 target = 0.189079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.139875 restraints weight = 21542.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.136092 restraints weight = 18485.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.137785 restraints weight = 19729.736| |-----------------------------------------------------------------------------| r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.2378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 18192 Z= 0.144 Angle : 0.623 13.244 24735 Z= 0.299 Chirality : 0.042 0.200 2727 Planarity : 0.004 0.041 3081 Dihedral : 4.388 38.526 2616 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 2.38 % Allowed : 14.97 % Favored : 82.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.18), residues: 2163 helix: 1.72 (0.16), residues: 1161 sheet: -0.62 (0.38), residues: 165 loop : -1.17 (0.20), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 784 HIS 0.004 0.001 HIS A 514 PHE 0.011 0.001 PHE B 397 TYR 0.016 0.002 TYR A 621 ARG 0.011 0.001 ARG A 323 Details of bonding type rmsd link_BETA1-4 : bond 0.00393 ( 6) link_BETA1-4 : angle 2.85347 ( 18) hydrogen bonds : bond 0.03509 ( 854) hydrogen bonds : angle 3.75189 ( 2535) covalent geometry : bond 0.00351 (18186) covalent geometry : angle 0.61825 (24717) *********************** 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 329 residues out of total 1890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 284 time to evaluate : 1.912 Fit side-chains REVERT: A 237 GLN cc_start: 0.7982 (mp10) cc_final: 0.7652 (pm20) REVERT: A 360 MET cc_start: 0.8414 (ttp) cc_final: 0.8148 (ttp) REVERT: A 389 GLU cc_start: 0.7994 (mm-30) cc_final: 0.7685 (mm-30) REVERT: A 546 ASN cc_start: 0.8504 (t0) cc_final: 0.8187 (t0) REVERT: A 675 MET cc_start: 0.6463 (tmm) cc_final: 0.5859 (tmm) REVERT: A 757 ILE cc_start: 0.8953 (tt) cc_final: 0.8594 (mt) REVERT: A 886 ASN cc_start: 0.8513 (t0) cc_final: 0.7904 (t0) REVERT: B 237 GLN cc_start: 0.8098 (mp10) cc_final: 0.7632 (mp10) REVERT: B 323 ARG cc_start: 0.7487 (ptt-90) cc_final: 0.7156 (ptt90) REVERT: B 389 GLU cc_start: 0.7908 (mm-30) cc_final: 0.7568 (mm-30) REVERT: B 807 LYS cc_start: 0.7347 (mttt) cc_final: 0.6753 (mtpp) REVERT: B 847 MET cc_start: 0.8912 (pmm) cc_final: 0.8531 (pmm) REVERT: C 237 GLN cc_start: 0.7897 (mp10) cc_final: 0.7661 (pm20) REVERT: C 373 ASP cc_start: 0.8240 (t0) cc_final: 0.7812 (t70) REVERT: C 403 ILE cc_start: 0.8232 (mm) cc_final: 0.7868 (mm) REVERT: C 474 LYS cc_start: 0.7798 (mttp) cc_final: 0.7590 (mmtp) REVERT: C 908 LYS cc_start: 0.8366 (ttpt) cc_final: 0.7977 (tttm) outliers start: 45 outliers final: 41 residues processed: 306 average time/residue: 0.3181 time to fit residues: 146.8664 Evaluate side-chains 320 residues out of total 1890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 279 time to evaluate : 1.861 ------------------------------------------------------------------------------- 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 567 VAL 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 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 242 LYS 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 842 THR Chi-restraints excluded: chain C residue 360 MET Chi-restraints excluded: chain C residue 417 ASP 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 773 ASN 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: 10.0000 chunk 8 optimal weight: 5.9990 chunk 206 optimal weight: 1.9990 chunk 185 optimal weight: 0.7980 chunk 117 optimal weight: 3.9990 chunk 203 optimal weight: 5.9990 chunk 63 optimal weight: 0.4980 chunk 193 optimal weight: 1.9990 chunk 114 optimal weight: 0.4980 chunk 179 optimal weight: 0.7980 chunk 11 optimal weight: 0.2980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.3940 r_free = 0.3940 target = 0.190507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.141909 restraints weight = 21464.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.136381 restraints weight = 17147.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.138436 restraints weight = 20714.724| |-----------------------------------------------------------------------------| r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 moved from start: 0.2470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 18192 Z= 0.118 Angle : 0.608 13.961 24735 Z= 0.290 Chirality : 0.041 0.199 2727 Planarity : 0.004 0.036 3081 Dihedral : 4.071 25.561 2616 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.06 % Allowed : 15.50 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.18), residues: 2163 helix: 1.79 (0.16), residues: 1161 sheet: -0.56 (0.39), residues: 165 loop : -1.12 (0.20), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 784 HIS 0.004 0.001 HIS B 514 PHE 0.011 0.001 PHE B 397 TYR 0.019 0.001 TYR C 608 ARG 0.011 0.001 ARG A 323 Details of bonding type rmsd link_BETA1-4 : bond 0.00398 ( 6) link_BETA1-4 : angle 2.38004 ( 18) hydrogen bonds : bond 0.03243 ( 854) hydrogen bonds : angle 3.67726 ( 2535) covalent geometry : bond 0.00280 (18186) covalent geometry : angle 0.60439 (24717) ********************** 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 326 residues out of total 1890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 287 time to evaluate : 2.102 Fit side-chains revert: symmetry clash REVERT: A 237 GLN cc_start: 0.7996 (mp10) cc_final: 0.7632 (pm20) REVERT: A 360 MET cc_start: 0.8359 (ttp) cc_final: 0.8060 (ttp) REVERT: A 389 GLU cc_start: 0.8021 (mm-30) cc_final: 0.7713 (mm-30) REVERT: A 546 ASN cc_start: 0.8532 (t0) cc_final: 0.8198 (t0) REVERT: A 675 MET cc_start: 0.6402 (tmm) cc_final: 0.5763 (tmm) REVERT: A 757 ILE cc_start: 0.8953 (tt) cc_final: 0.8567 (mt) REVERT: A 784 TRP cc_start: 0.8060 (m-10) cc_final: 0.7615 (m-10) REVERT: A 883 TRP cc_start: 0.8413 (t60) cc_final: 0.8212 (t60) REVERT: A 886 ASN cc_start: 0.8500 (t0) cc_final: 0.7914 (t0) REVERT: B 237 GLN cc_start: 0.8057 (mp10) cc_final: 0.7625 (pm20) REVERT: B 323 ARG cc_start: 0.7457 (ptt-90) cc_final: 0.7133 (ptt90) REVERT: B 807 LYS cc_start: 0.7271 (mttt) cc_final: 0.6650 (mtpp) REVERT: C 237 GLN cc_start: 0.7826 (mp10) cc_final: 0.7615 (pm20) REVERT: C 386 GLU cc_start: 0.7012 (mm-30) cc_final: 0.6727 (tp30) REVERT: C 403 ILE cc_start: 0.8123 (mm) cc_final: 0.7741 (mm) REVERT: C 908 LYS cc_start: 0.8401 (ttpt) cc_final: 0.8007 (tttm) outliers start: 39 outliers final: 38 residues processed: 307 average time/residue: 0.3082 time to fit residues: 142.5591 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 : 1.939 ------------------------------------------------------------------------------- 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 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 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 242 LYS 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 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 360 MET 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 157 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 150 optimal weight: 0.9990 chunk 44 optimal weight: 0.0040 chunk 93 optimal weight: 1.9990 chunk 172 optimal weight: 0.9980 chunk 156 optimal weight: 0.5980 chunk 179 optimal weight: 3.9990 chunk 122 optimal weight: 2.9990 chunk 197 optimal weight: 0.6980 chunk 125 optimal weight: 0.6980 overall best weight: 0.5992 ------------------------------------------------------------------------------- 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 571 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 = 0.3974 r_free = 0.3974 target = 0.193714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.145309 restraints weight = 21500.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.141028 restraints weight = 18081.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.142697 restraints weight = 21772.365| |-----------------------------------------------------------------------------| r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.2534 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= 0.121 Angle : 0.611 13.685 24735 Z= 0.292 Chirality : 0.041 0.275 2727 Planarity : 0.004 0.053 3081 Dihedral : 3.942 17.978 2616 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 2.17 % Allowed : 15.61 % Favored : 82.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.18), residues: 2163 helix: 1.82 (0.16), residues: 1164 sheet: -0.51 (0.39), residues: 165 loop : -1.08 (0.20), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 784 HIS 0.004 0.001 HIS B 514 PHE 0.011 0.001 PHE B 397 TYR 0.015 0.001 TYR A 621 ARG 0.010 0.001 ARG A 323 Details of bonding type rmsd link_BETA1-4 : bond 0.00386 ( 6) link_BETA1-4 : angle 2.32408 ( 18) hydrogen bonds : bond 0.03223 ( 854) hydrogen bonds : angle 3.66699 ( 2535) covalent geometry : bond 0.00291 (18186) covalent geometry : angle 0.60798 (24717) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6879.40 seconds wall clock time: 124 minutes 53.45 seconds (7493.45 seconds total)