Starting phenix.real_space_refine on Sat Jul 4 02:35:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7d5k_30583/07_2026/7d5k_30583.cif Found real_map, /net/cci-nas-00/data/ceres_data/7d5k_30583/07_2026/7d5k_30583.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7d5k_30583/07_2026/7d5k_30583.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7d5k_30583/07_2026/7d5k_30583.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7d5k_30583/07_2026/7d5k_30583.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7d5k_30583/07_2026/7d5k_30583.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7d5k_30583/07_2026/7d5k_30583.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7d5k_30583/07_2026/7d5k_30583.map" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.052 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 102 5.16 5 C 11559 2.51 5 N 2928 2.21 5 O 3078 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 48 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 17667 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 5843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 727, 5843 Classifications: {'peptide': 727} Link IDs: {'PTRANS': 47, 'TRANS': 679} Chain breaks: 2 Chain: "B" Number of atoms: 5843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 727, 5843 Classifications: {'peptide': 727} Link IDs: {'PTRANS': 47, 'TRANS': 679} Chain breaks: 2 Chain: "C" Number of atoms: 5843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 727, 5843 Classifications: {'peptide': 727} Link IDs: {'PTRANS': 47, 'TRANS': 679} Chain breaks: 2 Chain: "D" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 23 Unusual residues: {'BGC': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen 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 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 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 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 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 chiralities: 1 Time building chain proxies: 3.74, per 1000 atoms: 0.21 Number of scatterers: 17667 At special positions: 0 Unit cell: (136.962, 138.049, 109.787, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 102 16.00 O 3078 8.00 N 2928 7.00 C 11559 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " BGC D 1 " - " BGC D 2 " " BGC E 1 " - " BGC E 2 " " BGC F 1 " - " BGC F 2 " " BGC G 1 " - " BGC G 2 " " BGC H 1 " - " BGC H 2 " " BGC I 1 " - " BGC I 2 " Time building additional restraints: 1.62 Conformation dependent library (CDL) restraints added in 851.4 milliseconds 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4068 Finding SS restraints... Secondary structure from input PDB file: 87 helices and 9 sheets defined 57.1% alpha, 6.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.51 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: 2.66 Time building geometry restraints manager: 2.15 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 - 17.36: 9728 17.36 - 34.72: 697 34.72 - 52.09: 129 52.09 - 69.45: 48 69.45 - 86.81: 24 Dihedral angle restraints: 10626 sinusoidal: 4308 harmonic: 6318 Sorted by residual: dihedral pdb=" CA LEU A 987 " pdb=" C LEU A 987 " pdb=" N TYR A 988 " pdb=" CA TYR A 988 " ideal model delta harmonic sigma weight residual -180.00 -161.50 -18.50 0 5.00e+00 4.00e-02 1.37e+01 dihedral pdb=" CA LEU B 987 " pdb=" C LEU B 987 " pdb=" N TYR B 988 " pdb=" CA TYR B 988 " ideal model delta harmonic sigma weight residual 180.00 -161.50 -18.50 0 5.00e+00 4.00e-02 1.37e+01 dihedral pdb=" CA LEU C 987 " pdb=" C LEU C 987 " pdb=" N TYR C 988 " pdb=" CA TYR C 988 " ideal model delta harmonic sigma weight residual -180.00 -161.51 -18.49 0 5.00e+00 4.00e-02 1.37e+01 ... (remaining 10623 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.030 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: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 16.400 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 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 : 13.773 86.810 6558 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.77 % Favored : 92.23 % Rotamer: Outliers : 0.79 % Allowed : 1.43 % Favored : 97.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.18), residues: 2163 helix: 0.90 (0.15), residues: 1167 sheet: -1.15 (0.38), residues: 147 loop : -1.21 (0.21), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 795 TYR 0.020 0.002 TYR B 758 PHE 0.034 0.001 PHE B 306 TRP 0.024 0.001 TRP C 800 HIS 0.003 0.001 HIS A 986 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.16 (18186) covalent geometry : angle 0.69063 / 0.36 (24717) hydrogen bonds : bond 0.12407 / 8.90 ( 854) hydrogen bonds : angle 5.06698 / 3.75 ( 2535) link_BETA1-4 : bond 0.00218 / 0.13 ( 6) link_BETA1-4 : angle 2.12977 / 1.29 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 1890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 330 time to evaluate : 0.638 Fit side-chains REVERT: A 237 GLN cc_start: 0.7938 (mp10) cc_final: 0.7581 (mp10) REVERT: A 241 ARG cc_start: 0.7155 (ttp-110) cc_final: 0.6884 (ttm110) REVERT: A 360 MET cc_start: 0.8296 (ttp) cc_final: 0.7985 (ttp) REVERT: A 434 MET cc_start: 0.8289 (tpp) cc_final: 0.8002 (tpp) REVERT: A 908 LYS cc_start: 0.7816 (ttpt) cc_final: 0.6755 (ttpt) REVERT: B 237 GLN cc_start: 0.7931 (mp10) cc_final: 0.7305 (mp10) REVERT: B 343 MET cc_start: 0.7835 (mmm) cc_final: 0.7564 (mmm) REVERT: B 389 GLU cc_start: 0.8246 (mm-30) cc_final: 0.7395 (mm-30) REVERT: B 474 LYS cc_start: 0.7779 (mttp) cc_final: 0.7483 (mmmm) REVERT: B 555 MET cc_start: 0.8951 (mmt) cc_final: 0.8712 (mmm) REVERT: B 786 LEU cc_start: 0.8392 (tp) cc_final: 0.8119 (tp) REVERT: B 847 MET cc_start: 0.9007 (pmm) cc_final: 0.8315 (pmm) REVERT: C 237 GLN cc_start: 0.8099 (mp10) cc_final: 0.7809 (mp10) REVERT: C 313 TYR cc_start: 0.8073 (m-10) cc_final: 0.7475 (m-80) REVERT: C 323 ARG cc_start: 0.7563 (ptt180) cc_final: 0.7233 (ptt90) REVERT: C 474 LYS cc_start: 0.7801 (mttp) cc_final: 0.7565 (mmtp) REVERT: C 795 ARG cc_start: 0.7160 (ptt-90) cc_final: 0.6827 (ptt-90) outliers start: 15 outliers final: 3 residues processed: 335 average time/residue: 0.1409 time to fit residues: 70.5017 Evaluate side-chains 287 residues out of total 1890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 284 time to evaluate : 0.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 493 GLU Chi-restraints excluded: chain B residue 493 GLU Chi-restraints excluded: chain C residue 493 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 0.7980 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 0.0370 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 0.3980 chunk 103 optimal weight: 0.7980 chunk 200 optimal weight: 0.0370 chunk 212 optimal weight: 9.9990 chunk 77 optimal weight: 2.9990 overall best weight: 0.4136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 513 HIS ** A 898 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 486 GLN ** B 898 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 898 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.192285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.143834 restraints weight = 21216.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.142915 restraints weight = 17746.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.143688 restraints weight = 21312.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.144731 restraints weight = 12510.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.145217 restraints weight = 10840.397| |-----------------------------------------------------------------------------| r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.1074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18192 Z= 0.127 Angle : 0.608 7.610 24735 Z= 0.303 Chirality : 0.043 0.184 2727 Planarity : 0.004 0.045 3081 Dihedral : 5.511 95.059 2379 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 0.95 % Allowed : 7.57 % Favored : 91.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.18), residues: 2163 helix: 1.13 (0.15), residues: 1170 sheet: -1.09 (0.37), residues: 162 loop : -1.18 (0.20), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 795 TYR 0.018 0.001 TYR C 758 PHE 0.026 0.001 PHE B 306 TRP 0.013 0.001 TRP C 800 HIS 0.003 0.001 HIS A 986 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 (18186) covalent geometry : angle 0.60617 / 0.30 (24717) hydrogen bonds : bond 0.04033 / 2.67 ( 854) hydrogen bonds : angle 4.19416 / 3.10 ( 2535) link_BETA1-4 : bond 0.00242 / 0.14 ( 6) link_BETA1-4 : angle 1.65124 / 1.04 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 1890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 316 time to evaluate : 0.657 Fit side-chains REVERT: A 237 GLN cc_start: 0.7858 (mp10) cc_final: 0.7496 (mp10) REVERT: A 360 MET cc_start: 0.8357 (ttp) cc_final: 0.8019 (ttp) REVERT: A 389 GLU cc_start: 0.8097 (mm-30) cc_final: 0.7551 (mm-30) REVERT: A 434 MET cc_start: 0.8388 (tpp) cc_final: 0.8130 (tpp) REVERT: A 493 GLU cc_start: 0.7852 (mm-30) cc_final: 0.7633 (mm-30) REVERT: A 527 SER cc_start: 0.8940 (m) cc_final: 0.8724 (m) REVERT: A 546 ASN cc_start: 0.8513 (t0) cc_final: 0.8178 (t0) REVERT: A 784 TRP cc_start: 0.7257 (m-10) cc_final: 0.6885 (m-10) REVERT: B 389 GLU cc_start: 0.8016 (mm-30) cc_final: 0.7538 (mm-30) REVERT: B 527 SER cc_start: 0.9004 (m) cc_final: 0.8776 (m) REVERT: B 807 LYS cc_start: 0.7194 (mttt) cc_final: 0.6599 (mtpp) REVERT: C 474 LYS cc_start: 0.7828 (mttp) cc_final: 0.7609 (mmtp) REVERT: C 692 THR cc_start: 0.8102 (m) cc_final: 0.7772 (p) REVERT: C 783 ARG cc_start: 0.7192 (mtp-110) cc_final: 0.6958 (mtp-110) REVERT: C 795 ARG cc_start: 0.7088 (ptt-90) cc_final: 0.6749 (ptt-90) REVERT: C 847 MET cc_start: 0.8911 (pmm) cc_final: 0.8511 (pmm) REVERT: C 908 LYS cc_start: 0.7795 (ttpt) cc_final: 0.7576 (ttpt) outliers start: 18 outliers final: 10 residues processed: 321 average time/residue: 0.1351 time to fit residues: 65.0703 Evaluate side-chains 295 residues out of total 1890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 285 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 490 HIS Chi-restraints excluded: chain A residue 718 ILE Chi-restraints excluded: chain A residue 719 SER Chi-restraints excluded: chain B residue 679 ASN Chi-restraints excluded: chain B residue 694 THR Chi-restraints excluded: chain C residue 443 VAL Chi-restraints excluded: chain C residue 679 ASN Chi-restraints excluded: chain C residue 694 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 177 optimal weight: 0.9990 chunk 205 optimal weight: 0.9990 chunk 32 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 chunk 104 optimal weight: 0.9990 chunk 83 optimal weight: 0.9990 chunk 28 optimal weight: 3.9990 chunk 144 optimal weight: 4.9990 chunk 84 optimal weight: 0.9990 chunk 102 optimal weight: 0.9990 chunk 51 optimal weight: 0.3980 overall best weight: 0.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3931 r_free = 0.3931 target = 0.189735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.140971 restraints weight = 21604.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.136026 restraints weight = 16819.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.137439 restraints weight = 22062.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.139107 restraints weight = 12664.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.140290 restraints weight = 10472.299| |-----------------------------------------------------------------------------| r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.1436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 18192 Z= 0.142 Angle : 0.597 7.503 24735 Z= 0.294 Chirality : 0.042 0.185 2727 Planarity : 0.004 0.037 3081 Dihedral : 4.234 18.131 2370 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 1.53 % Allowed : 10.00 % Favored : 88.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.18), residues: 2163 helix: 1.25 (0.16), residues: 1176 sheet: -0.80 (0.38), residues: 165 loop : -1.18 (0.20), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 795 TYR 0.018 0.002 TYR B 758 PHE 0.021 0.001 PHE C 306 TRP 0.013 0.001 TRP B 800 HIS 0.005 0.001 HIS B 514 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.14 (18186) covalent geometry : angle 0.59519 / 0.29 (24717) hydrogen bonds : bond 0.03964 / 2.65 ( 854) hydrogen bonds : angle 4.03480 / 2.96 ( 2535) link_BETA1-4 : bond 0.00114 / 0.07 ( 6) link_BETA1-4 : angle 2.03300 / 1.23 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 1890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 300 time to evaluate : 0.660 Fit side-chains revert: symmetry clash REVERT: A 237 GLN cc_start: 0.7920 (mp10) cc_final: 0.7359 (mp10) REVERT: A 360 MET cc_start: 0.8430 (ttp) cc_final: 0.8198 (ttp) REVERT: A 373 ASP cc_start: 0.8420 (t0) cc_final: 0.8147 (t0) REVERT: A 389 GLU cc_start: 0.8040 (mm-30) cc_final: 0.7673 (mm-30) REVERT: A 527 SER cc_start: 0.8958 (m) cc_final: 0.8710 (m) REVERT: A 546 ASN cc_start: 0.8537 (t0) cc_final: 0.8171 (t0) REVERT: A 553 GLU cc_start: 0.7746 (tt0) cc_final: 0.7473 (mt-10) REVERT: A 886 ASN cc_start: 0.8320 (t0) cc_final: 0.7714 (t0) REVERT: B 237 GLN cc_start: 0.7987 (mp10) cc_final: 0.7566 (mp10) REVERT: B 389 GLU cc_start: 0.7977 (mm-30) cc_final: 0.7575 (mm-30) REVERT: B 807 LYS cc_start: 0.7151 (mttt) cc_final: 0.6543 (mtpp) REVERT: C 237 GLN cc_start: 0.8054 (mp10) cc_final: 0.7705 (pm20) REVERT: C 373 ASP cc_start: 0.8439 (t0) cc_final: 0.8173 (t0) REVERT: C 403 ILE cc_start: 0.8253 (mm) cc_final: 0.7892 (mm) outliers start: 29 outliers final: 23 residues processed: 308 average time/residue: 0.1347 time to fit residues: 63.1092 Evaluate side-chains 293 residues out of total 1890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 270 time to evaluate : 0.651 ------------------------------------------------------------------------------- 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 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 A residue 891 VAL 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 150 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 147 optimal weight: 4.9990 chunk 127 optimal weight: 3.9990 chunk 63 optimal weight: 0.0170 chunk 132 optimal weight: 5.9990 chunk 1 optimal weight: 7.9990 chunk 144 optimal weight: 4.9990 chunk 213 optimal weight: 0.9990 chunk 34 optimal weight: 5.9990 overall best weight: 2.2026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 513 HIS A 538 ASN ** A 898 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 486 GLN B 513 HIS B 677 GLN ** B 898 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 538 ASN C 677 GLN ** C 898 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.182901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.133220 restraints weight = 21462.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.129480 restraints weight = 17702.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.130566 restraints weight = 22418.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.132028 restraints weight = 12295.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.135102 restraints weight = 10156.806| |-----------------------------------------------------------------------------| r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.1991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.048 18192 Z= 0.277 Angle : 0.722 7.444 24735 Z= 0.361 Chirality : 0.047 0.194 2727 Planarity : 0.005 0.047 3081 Dihedral : 4.849 23.478 2370 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 3.02 % Allowed : 11.75 % Favored : 85.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.18), residues: 2163 helix: 1.12 (0.15), residues: 1152 sheet: -1.12 (0.36), residues: 165 loop : -1.39 (0.20), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 777 TYR 0.023 0.002 TYR C 758 PHE 0.018 0.002 PHE C 306 TRP 0.017 0.002 TRP B 800 HIS 0.007 0.002 HIS B 716 Details of bonding type rmsd/Z covalent geometry : bond 0.00674 / 0.28 (18186) covalent geometry : angle 0.71691 / 0.36 (24717) hydrogen bonds : bond 0.05024 / 3.37 ( 854) hydrogen bonds : angle 4.38799 / 3.19 ( 2535) link_BETA1-4 : bond 0.00364 / 0.20 ( 6) link_BETA1-4 : angle 3.32495 / 1.98 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 1890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 290 time to evaluate : 0.630 Fit side-chains REVERT: A 237 GLN cc_start: 0.8038 (mp10) cc_final: 0.7537 (mp10) REVERT: A 373 ASP cc_start: 0.8552 (t0) cc_final: 0.8260 (t0) REVERT: A 389 GLU cc_start: 0.8134 (mm-30) cc_final: 0.7725 (mm-30) REVERT: A 553 GLU cc_start: 0.7930 (tt0) cc_final: 0.7635 (mt-10) REVERT: A 886 ASN cc_start: 0.8725 (t0) cc_final: 0.8033 (t0) REVERT: B 237 GLN cc_start: 0.8061 (mp10) cc_final: 0.7580 (mp10) REVERT: B 373 ASP cc_start: 0.8632 (t0) cc_final: 0.8293 (t0) REVERT: B 389 GLU cc_start: 0.8053 (mm-30) cc_final: 0.7700 (mm-30) REVERT: B 807 LYS cc_start: 0.7339 (mttt) cc_final: 0.6737 (mtpp) REVERT: C 237 GLN cc_start: 0.8196 (mp10) cc_final: 0.7544 (mp10) REVERT: C 373 ASP cc_start: 0.8530 (t0) cc_final: 0.8256 (t0) outliers start: 57 outliers final: 46 residues processed: 320 average time/residue: 0.1369 time to fit residues: 67.0145 Evaluate side-chains 327 residues out of total 1890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 281 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 490 HIS Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 611 THR Chi-restraints excluded: chain A residue 684 PHE Chi-restraints excluded: chain A residue 694 THR Chi-restraints excluded: chain A residue 718 ILE Chi-restraints excluded: chain A residue 719 SER Chi-restraints excluded: chain A residue 726 THR Chi-restraints excluded: chain A residue 786 LEU 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 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 773 ASN Chi-restraints excluded: chain B residue 940 LEU Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 423 VAL 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 538 ASN Chi-restraints excluded: chain C residue 567 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 718 ILE Chi-restraints excluded: chain C residue 719 SER Chi-restraints excluded: chain C residue 726 THR Chi-restraints excluded: chain C residue 891 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 189 optimal weight: 0.7980 chunk 165 optimal weight: 0.7980 chunk 96 optimal weight: 1.9990 chunk 129 optimal weight: 20.0000 chunk 44 optimal weight: 0.6980 chunk 195 optimal weight: 0.4980 chunk 119 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 15 optimal weight: 0.9980 chunk 97 optimal weight: 0.9980 chunk 121 optimal weight: 4.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3899 r_free = 0.3899 target = 0.186456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.136361 restraints weight = 21450.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.132174 restraints weight = 16853.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.133585 restraints weight = 21022.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.134814 restraints weight = 12067.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.138098 restraints weight = 10237.726| |-----------------------------------------------------------------------------| r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.1998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 18192 Z= 0.137 Angle : 0.614 7.742 24735 Z= 0.302 Chirality : 0.043 0.273 2727 Planarity : 0.004 0.035 3081 Dihedral : 4.453 21.291 2370 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 2.22 % Allowed : 13.49 % Favored : 84.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.18), residues: 2163 helix: 1.35 (0.16), residues: 1155 sheet: -0.92 (0.38), residues: 165 loop : -1.31 (0.20), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 777 TYR 0.015 0.002 TYR B 569 PHE 0.013 0.001 PHE A 397 TRP 0.015 0.001 TRP C 800 HIS 0.003 0.001 HIS B 716 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 (18186) covalent geometry : angle 0.61098 / 0.30 (24717) hydrogen bonds : bond 0.04042 / 2.70 ( 854) hydrogen bonds : angle 4.09653 / 3.00 ( 2535) link_BETA1-4 : bond 0.00156 / 0.10 ( 6) link_BETA1-4 : angle 2.35852 / 1.41 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 1890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 305 time to evaluate : 0.673 Fit side-chains REVERT: A 237 GLN cc_start: 0.7959 (mp10) cc_final: 0.7500 (mp10) REVERT: A 360 MET cc_start: 0.8431 (ttp) cc_final: 0.8148 (ttp) REVERT: A 373 ASP cc_start: 0.8432 (t0) cc_final: 0.8086 (t0) REVERT: A 389 GLU cc_start: 0.8057 (mm-30) cc_final: 0.7657 (mm-30) REVERT: A 527 SER cc_start: 0.8791 (m) cc_final: 0.8533 (m) REVERT: A 546 ASN cc_start: 0.8437 (t0) cc_final: 0.8150 (t0) REVERT: A 553 GLU cc_start: 0.7762 (tt0) cc_final: 0.7546 (mt-10) REVERT: A 886 ASN cc_start: 0.8689 (t0) cc_final: 0.8010 (t0) REVERT: B 237 GLN cc_start: 0.8019 (mp10) cc_final: 0.7571 (mp10) REVERT: B 389 GLU cc_start: 0.8000 (mm-30) cc_final: 0.7664 (mm-30) REVERT: B 511 PHE cc_start: 0.7649 (m-80) cc_final: 0.7330 (m-80) REVERT: C 237 GLN cc_start: 0.8043 (mp10) cc_final: 0.7833 (pm20) REVERT: C 386 GLU cc_start: 0.7009 (mm-30) cc_final: 0.6679 (tp30) REVERT: C 403 ILE cc_start: 0.8224 (mm) cc_final: 0.7975 (mm) REVERT: C 847 MET cc_start: 0.8961 (pmm) cc_final: 0.8654 (pmm) REVERT: C 908 LYS cc_start: 0.8010 (ttpt) cc_final: 0.7184 (tttt) outliers start: 42 outliers final: 33 residues processed: 326 average time/residue: 0.1405 time to fit residues: 69.4096 Evaluate side-chains 319 residues out of total 1890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 286 time to evaluate : 0.650 ------------------------------------------------------------------------------- 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 423 VAL Chi-restraints excluded: chain A residue 443 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 891 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 940 LEU Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain C residue 417 ASP Chi-restraints excluded: chain C residue 443 VAL Chi-restraints excluded: chain C residue 490 HIS Chi-restraints excluded: chain C residue 600 LEU Chi-restraints excluded: chain C residue 603 ILE Chi-restraints excluded: chain C residue 611 THR Chi-restraints excluded: chain C residue 679 ASN Chi-restraints excluded: chain C residue 684 PHE Chi-restraints excluded: chain C residue 694 THR Chi-restraints excluded: chain C residue 719 SER Chi-restraints excluded: chain C residue 773 ASN Chi-restraints excluded: chain C residue 891 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 210 optimal weight: 9.9990 chunk 117 optimal weight: 3.9990 chunk 12 optimal weight: 0.7980 chunk 161 optimal weight: 0.7980 chunk 162 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 17 optimal weight: 0.0980 chunk 164 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 chunk 163 optimal weight: 1.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3911 r_free = 0.3911 target = 0.187680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.138320 restraints weight = 21329.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.132510 restraints weight = 17108.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.133786 restraints weight = 21874.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.134725 restraints weight = 12377.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.136899 restraints weight = 10321.126| |-----------------------------------------------------------------------------| r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.2126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 18192 Z= 0.131 Angle : 0.596 7.857 24735 Z= 0.292 Chirality : 0.042 0.233 2727 Planarity : 0.004 0.080 3081 Dihedral : 4.260 19.847 2370 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 2.43 % Allowed : 14.50 % Favored : 83.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.18), residues: 2163 helix: 1.48 (0.16), residues: 1161 sheet: -0.84 (0.38), residues: 165 loop : -1.26 (0.20), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 323 TYR 0.016 0.001 TYR C 608 PHE 0.012 0.001 PHE A 397 TRP 0.017 0.001 TRP C 800 HIS 0.003 0.001 HIS C 514 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.13 (18186) covalent geometry : angle 0.59342 / 0.29 (24717) hydrogen bonds : bond 0.03681 / 2.45 ( 854) hydrogen bonds : angle 3.93320 / 2.88 ( 2535) link_BETA1-4 : bond 0.00173 / 0.11 ( 6) link_BETA1-4 : angle 2.18901 / 1.31 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 1890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 298 time to evaluate : 0.649 Fit side-chains REVERT: A 237 GLN cc_start: 0.7983 (mp10) cc_final: 0.7507 (mp10) REVERT: A 360 MET cc_start: 0.8358 (ttp) cc_final: 0.8054 (ttp) REVERT: A 373 ASP cc_start: 0.8448 (t0) cc_final: 0.7989 (t0) REVERT: A 386 GLU cc_start: 0.7062 (mm-30) cc_final: 0.6631 (tp30) REVERT: A 389 GLU cc_start: 0.8026 (mm-30) cc_final: 0.7726 (mm-30) REVERT: A 527 SER cc_start: 0.8781 (m) cc_final: 0.8563 (m) REVERT: A 542 ASP cc_start: 0.7839 (p0) cc_final: 0.7626 (p0) REVERT: A 546 ASN cc_start: 0.8464 (t0) cc_final: 0.8171 (t0) REVERT: A 886 ASN cc_start: 0.8694 (t0) cc_final: 0.7995 (t0) REVERT: A 908 LYS cc_start: 0.6673 (ttpt) cc_final: 0.6467 (ttpt) REVERT: B 237 GLN cc_start: 0.8063 (mp10) cc_final: 0.7628 (mp10) REVERT: B 241 ARG cc_start: 0.8144 (ttm110) cc_final: 0.7715 (ttp-110) REVERT: B 323 ARG cc_start: 0.7394 (ptt-90) cc_final: 0.7048 (ptt90) REVERT: B 389 GLU cc_start: 0.7970 (mm-30) cc_final: 0.7638 (mm-30) REVERT: B 511 PHE cc_start: 0.7630 (m-80) cc_final: 0.7347 (m-80) REVERT: C 237 GLN cc_start: 0.8057 (mp10) cc_final: 0.7758 (pm20) REVERT: C 386 GLU cc_start: 0.7002 (mm-30) cc_final: 0.6693 (tp30) REVERT: C 403 ILE cc_start: 0.8279 (mm) cc_final: 0.7997 (mm) REVERT: C 847 MET cc_start: 0.8983 (pmm) cc_final: 0.8717 (pmm) outliers start: 46 outliers final: 36 residues processed: 324 average time/residue: 0.1386 time to fit residues: 68.3171 Evaluate side-chains 321 residues out of total 1890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 285 time to evaluate : 0.657 ------------------------------------------------------------------------------- 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 423 VAL Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 455 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 891 VAL 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 751 CYS Chi-restraints excluded: chain B residue 773 ASN 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 490 HIS Chi-restraints excluded: chain C residue 600 LEU Chi-restraints excluded: chain C residue 611 THR Chi-restraints excluded: chain C residue 679 ASN Chi-restraints excluded: chain C residue 684 PHE Chi-restraints excluded: chain C residue 694 THR Chi-restraints excluded: chain C residue 719 SER Chi-restraints excluded: chain C residue 726 THR Chi-restraints excluded: chain C residue 891 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 118 optimal weight: 0.6980 chunk 77 optimal weight: 3.9990 chunk 179 optimal weight: 0.3980 chunk 120 optimal weight: 0.0570 chunk 163 optimal weight: 0.9990 chunk 119 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 85 optimal weight: 0.8980 chunk 134 optimal weight: 2.9990 chunk 214 optimal weight: 10.0000 chunk 64 optimal weight: 4.9990 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3964 r_free = 0.3964 target = 0.192552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.144096 restraints weight = 21477.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.140970 restraints weight = 19482.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.142703 restraints weight = 20877.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.142697 restraints weight = 13983.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.144865 restraints weight = 12612.551| |-----------------------------------------------------------------------------| r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.2236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 18192 Z= 0.121 Angle : 0.587 7.967 24735 Z= 0.287 Chirality : 0.042 0.254 2727 Planarity : 0.004 0.071 3081 Dihedral : 4.132 18.688 2370 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 2.43 % Allowed : 14.76 % Favored : 82.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.18), residues: 2163 helix: 1.58 (0.16), residues: 1161 sheet: -0.76 (0.38), residues: 165 loop : -1.20 (0.20), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 323 TYR 0.018 0.001 TYR A 621 PHE 0.012 0.001 PHE A 397 TRP 0.014 0.001 TRP C 800 HIS 0.004 0.001 HIS B 514 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.12 (18186) covalent geometry : angle 0.58504 / 0.29 (24717) hydrogen bonds : bond 0.03470 / 2.30 ( 854) hydrogen bonds : angle 3.84116 / 2.81 ( 2535) link_BETA1-4 : bond 0.00164 / 0.09 ( 6) link_BETA1-4 : angle 1.96703 / 1.18 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 1890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 297 time to evaluate : 0.683 Fit side-chains REVERT: A 237 GLN cc_start: 0.7925 (mp10) cc_final: 0.7582 (pm20) REVERT: A 360 MET cc_start: 0.8350 (ttp) cc_final: 0.8029 (ttp) REVERT: A 373 ASP cc_start: 0.8358 (t0) cc_final: 0.7907 (t0) REVERT: A 389 GLU cc_start: 0.7985 (mm-30) cc_final: 0.7686 (mm-30) REVERT: A 527 SER cc_start: 0.8689 (m) cc_final: 0.8481 (m) REVERT: A 546 ASN cc_start: 0.8482 (t0) cc_final: 0.8183 (t0) REVERT: A 694 THR cc_start: 0.8786 (OUTLIER) cc_final: 0.8567 (t) REVERT: A 784 TRP cc_start: 0.7866 (m-10) cc_final: 0.7446 (m-10) REVERT: A 886 ASN cc_start: 0.8662 (t0) cc_final: 0.7990 (t0) REVERT: B 237 GLN cc_start: 0.8000 (mp10) cc_final: 0.7624 (mp10) REVERT: B 241 ARG cc_start: 0.7965 (ttm110) cc_final: 0.7655 (ttp-110) REVERT: B 323 ARG cc_start: 0.7441 (ptt-90) cc_final: 0.7115 (ptt90) REVERT: B 389 GLU cc_start: 0.7886 (mm-30) cc_final: 0.7567 (mm-30) REVERT: B 511 PHE cc_start: 0.7686 (m-80) cc_final: 0.7447 (m-80) REVERT: B 807 LYS cc_start: 0.7181 (mttt) cc_final: 0.6597 (mtpp) REVERT: B 908 LYS cc_start: 0.7809 (ttpt) cc_final: 0.7524 (ttpt) REVERT: C 237 GLN cc_start: 0.8002 (mp10) cc_final: 0.7751 (pm20) REVERT: C 386 GLU cc_start: 0.6936 (mm-30) cc_final: 0.6629 (tp30) REVERT: C 403 ILE cc_start: 0.8214 (mm) cc_final: 0.7896 (mm) outliers start: 46 outliers final: 40 residues processed: 322 average time/residue: 0.1306 time to fit residues: 64.1825 Evaluate side-chains 332 residues out of total 1890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 291 time to evaluate : 0.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 423 VAL 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 694 THR Chi-restraints excluded: chain A residue 718 ILE Chi-restraints excluded: chain A residue 726 THR Chi-restraints excluded: chain A residue 842 THR Chi-restraints excluded: chain A residue 891 VAL Chi-restraints excluded: chain B residue 245 ILE Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 600 LEU Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain B residue 679 ASN Chi-restraints excluded: chain B residue 684 PHE Chi-restraints excluded: chain B residue 694 THR Chi-restraints excluded: chain B residue 719 SER Chi-restraints excluded: chain B residue 726 THR Chi-restraints excluded: chain B residue 842 THR Chi-restraints excluded: chain 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 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 715 ILE Chi-restraints excluded: chain C residue 719 SER Chi-restraints excluded: chain C residue 842 THR Chi-restraints excluded: chain C residue 891 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 26 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 211 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 chunk 130 optimal weight: 0.7980 chunk 163 optimal weight: 0.8980 chunk 13 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 6 optimal weight: 0.9990 chunk 21 optimal weight: 0.3980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3918 r_free = 0.3918 target = 0.188235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.139702 restraints weight = 21468.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.135962 restraints weight = 17224.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.137093 restraints weight = 21393.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.137962 restraints weight = 11762.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.141520 restraints weight = 10105.265| |-----------------------------------------------------------------------------| r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.2324 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= 0.136 Angle : 0.607 9.737 24735 Z= 0.294 Chirality : 0.042 0.285 2727 Planarity : 0.004 0.062 3081 Dihedral : 4.148 18.953 2370 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.65 % Allowed : 15.08 % Favored : 82.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.18), residues: 2163 helix: 1.63 (0.16), residues: 1161 sheet: -0.76 (0.38), residues: 165 loop : -1.18 (0.20), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 323 TYR 0.021 0.001 TYR A 621 PHE 0.011 0.001 PHE B 397 TRP 0.014 0.001 TRP B 800 HIS 0.004 0.001 HIS C 514 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.14 (18186) covalent geometry : angle 0.60402 / 0.29 (24717) hydrogen bonds : bond 0.03533 / 2.34 ( 854) hydrogen bonds : angle 3.83158 / 2.80 ( 2535) link_BETA1-4 : bond 0.00127 / 0.07 ( 6) link_BETA1-4 : angle 2.15021 / 1.29 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 1890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 293 time to evaluate : 0.777 Fit side-chains REVERT: A 237 GLN cc_start: 0.7905 (mp10) cc_final: 0.7578 (pm20) REVERT: A 360 MET cc_start: 0.8364 (ttp) cc_final: 0.8075 (ttp) REVERT: A 373 ASP cc_start: 0.8393 (t0) cc_final: 0.7874 (t0) REVERT: A 389 GLU cc_start: 0.8043 (mm-30) cc_final: 0.7725 (mm-30) REVERT: A 527 SER cc_start: 0.8765 (m) cc_final: 0.8525 (m) REVERT: A 546 ASN cc_start: 0.8464 (t0) cc_final: 0.8143 (t0) REVERT: A 675 MET cc_start: 0.6169 (tmm) cc_final: 0.5825 (tmm) REVERT: A 694 THR cc_start: 0.8803 (OUTLIER) cc_final: 0.8587 (t) REVERT: A 886 ASN cc_start: 0.8624 (t0) cc_final: 0.7965 (t0) REVERT: B 237 GLN cc_start: 0.7964 (mp10) cc_final: 0.7583 (pm20) REVERT: B 255 MET cc_start: 0.7283 (mtm) cc_final: 0.7060 (mtm) REVERT: B 323 ARG cc_start: 0.7518 (ptt-90) cc_final: 0.7195 (ptt90) REVERT: B 389 GLU cc_start: 0.7938 (mm-30) cc_final: 0.7606 (mm-30) REVERT: B 511 PHE cc_start: 0.7624 (m-80) cc_final: 0.7407 (m-80) REVERT: C 237 GLN cc_start: 0.7995 (mp10) cc_final: 0.7787 (pm20) REVERT: C 386 GLU cc_start: 0.7044 (mm-30) cc_final: 0.6714 (tp30) REVERT: C 403 ILE cc_start: 0.8288 (mm) cc_final: 0.7983 (mm) outliers start: 50 outliers final: 40 residues processed: 320 average time/residue: 0.1274 time to fit residues: 62.0350 Evaluate side-chains 327 residues out of total 1890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 286 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 455 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 842 THR Chi-restraints excluded: chain A residue 891 VAL 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 751 CYS Chi-restraints excluded: chain B residue 842 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 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 842 THR Chi-restraints excluded: chain C residue 891 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 193 optimal weight: 1.9990 chunk 145 optimal weight: 0.7980 chunk 151 optimal weight: 1.9990 chunk 135 optimal weight: 20.0000 chunk 0 optimal weight: 5.9990 chunk 47 optimal weight: 0.4980 chunk 160 optimal weight: 1.9990 chunk 155 optimal weight: 0.0770 chunk 41 optimal weight: 0.6980 chunk 38 optimal weight: 0.7980 chunk 133 optimal weight: 6.9990 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 513 HIS ** A 898 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 571 GLN B 898 HIS ** 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 = 0.3929 r_free = 0.3929 target = 0.189419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.140725 restraints weight = 21529.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.136560 restraints weight = 18139.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.137993 restraints weight = 21023.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.138679 restraints weight = 13150.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.141786 restraints weight = 11591.836| |-----------------------------------------------------------------------------| r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.2397 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= 0.119 Angle : 0.599 9.538 24735 Z= 0.288 Chirality : 0.042 0.346 2727 Planarity : 0.004 0.036 3081 Dihedral : 4.054 19.416 2370 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.43 % Allowed : 15.50 % Favored : 82.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.18), residues: 2163 helix: 1.71 (0.16), residues: 1161 sheet: -0.70 (0.38), residues: 165 loop : -1.14 (0.20), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 795 TYR 0.017 0.001 TYR C 608 PHE 0.012 0.001 PHE B 397 TRP 0.017 0.001 TRP B 784 HIS 0.004 0.001 HIS B 514 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.12 (18186) covalent geometry : angle 0.59680 / 0.29 (24717) hydrogen bonds : bond 0.03324 / 2.20 ( 854) hydrogen bonds : angle 3.75810 / 2.75 ( 2535) link_BETA1-4 : bond 0.00151 / 0.09 ( 6) link_BETA1-4 : angle 1.91307 / 1.15 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 1890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 293 time to evaluate : 0.556 Fit side-chains revert: symmetry clash REVERT: A 237 GLN cc_start: 0.7971 (mp10) cc_final: 0.7653 (pm20) REVERT: A 360 MET cc_start: 0.8339 (ttp) cc_final: 0.8050 (ttp) REVERT: A 373 ASP cc_start: 0.8323 (t0) cc_final: 0.7805 (t0) REVERT: A 389 GLU cc_start: 0.8028 (mm-30) cc_final: 0.7722 (mm-30) REVERT: A 527 SER cc_start: 0.8725 (m) cc_final: 0.8524 (m) REVERT: A 546 ASN cc_start: 0.8487 (t0) cc_final: 0.8173 (t0) REVERT: A 675 MET cc_start: 0.6070 (tmm) cc_final: 0.5719 (tmm) REVERT: A 694 THR cc_start: 0.8666 (OUTLIER) cc_final: 0.8428 (t) REVERT: A 784 TRP cc_start: 0.7988 (m-10) cc_final: 0.7615 (m-10) REVERT: A 886 ASN cc_start: 0.8642 (t0) cc_final: 0.8024 (t0) REVERT: B 237 GLN cc_start: 0.7980 (mp10) cc_final: 0.7616 (pm20) REVERT: B 323 ARG cc_start: 0.7511 (ptt-90) cc_final: 0.7184 (ptt90) REVERT: B 389 GLU cc_start: 0.7898 (mm-30) cc_final: 0.7561 (mm-30) REVERT: B 511 PHE cc_start: 0.7644 (m-80) cc_final: 0.7441 (m-80) REVERT: B 807 LYS cc_start: 0.7175 (mttt) cc_final: 0.6563 (mtpp) REVERT: C 386 GLU cc_start: 0.7011 (mm-30) cc_final: 0.6693 (tp30) REVERT: C 403 ILE cc_start: 0.8210 (mm) cc_final: 0.7881 (mm) outliers start: 46 outliers final: 40 residues processed: 317 average time/residue: 0.1287 time to fit residues: 62.3907 Evaluate side-chains 329 residues out of total 1890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 288 time to evaluate : 0.627 ------------------------------------------------------------------------------- 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 423 VAL Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 455 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 749 MET Chi-restraints excluded: chain A residue 842 THR Chi-restraints excluded: chain A residue 891 VAL Chi-restraints excluded: chain B residue 423 VAL 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 751 CYS Chi-restraints excluded: chain B residue 842 THR 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 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 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 167 optimal weight: 0.9990 chunk 4 optimal weight: 3.9990 chunk 144 optimal weight: 5.9990 chunk 102 optimal weight: 0.6980 chunk 193 optimal weight: 0.9980 chunk 189 optimal weight: 0.4980 chunk 164 optimal weight: 0.5980 chunk 95 optimal weight: 0.7980 chunk 47 optimal weight: 0.9990 chunk 36 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 513 HIS ** A 898 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 898 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.188730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.140145 restraints weight = 21241.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.135896 restraints weight = 17493.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.137406 restraints weight = 21001.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.138104 restraints weight = 13443.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.138794 restraints weight = 11983.605| |-----------------------------------------------------------------------------| r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.2469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18192 Z= 0.128 Angle : 0.607 9.716 24735 Z= 0.292 Chirality : 0.042 0.326 2727 Planarity : 0.004 0.036 3081 Dihedral : 4.042 20.197 2370 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 2.22 % Allowed : 15.93 % Favored : 81.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.18), residues: 2163 helix: 1.74 (0.16), residues: 1161 sheet: -0.70 (0.38), residues: 165 loop : -1.16 (0.20), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 323 TYR 0.018 0.001 TYR A 621 PHE 0.011 0.001 PHE B 397 TRP 0.016 0.001 TRP B 784 HIS 0.004 0.001 HIS B 514 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.13 (18186) covalent geometry : angle 0.60520 / 0.29 (24717) hydrogen bonds : bond 0.03349 / 2.22 ( 854) hydrogen bonds : angle 3.75683 / 2.75 ( 2535) link_BETA1-4 : bond 0.00146 / 0.09 ( 6) link_BETA1-4 : angle 2.01155 / 1.21 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 1890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 289 time to evaluate : 0.450 Fit side-chains revert: symmetry clash REVERT: A 237 GLN cc_start: 0.8028 (mp10) cc_final: 0.7690 (pm20) REVERT: A 360 MET cc_start: 0.8363 (ttp) cc_final: 0.8079 (ttp) REVERT: A 373 ASP cc_start: 0.8324 (t0) cc_final: 0.7820 (t0) REVERT: A 389 GLU cc_start: 0.7986 (mm-30) cc_final: 0.7654 (mm-30) REVERT: A 546 ASN cc_start: 0.8495 (t0) cc_final: 0.8174 (t0) REVERT: A 675 MET cc_start: 0.6303 (tmm) cc_final: 0.5964 (tmm) REVERT: A 694 THR cc_start: 0.8678 (OUTLIER) cc_final: 0.8460 (t) REVERT: A 886 ASN cc_start: 0.8529 (t0) cc_final: 0.7929 (t0) REVERT: B 237 GLN cc_start: 0.8033 (mp10) cc_final: 0.7650 (pm20) REVERT: B 323 ARG cc_start: 0.7515 (ptt-90) cc_final: 0.7033 (ptt90) REVERT: B 389 GLU cc_start: 0.7888 (mm-30) cc_final: 0.7570 (mm-30) REVERT: B 511 PHE cc_start: 0.7606 (m-80) cc_final: 0.7402 (m-80) REVERT: B 807 LYS cc_start: 0.7272 (mttt) cc_final: 0.6629 (mtpp) REVERT: C 386 GLU cc_start: 0.6992 (mm-30) cc_final: 0.6677 (tp30) REVERT: C 403 ILE cc_start: 0.8194 (mm) cc_final: 0.7867 (mm) outliers start: 42 outliers final: 40 residues processed: 312 average time/residue: 0.1135 time to fit residues: 54.1526 Evaluate side-chains 331 residues out of total 1890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 290 time to evaluate : 0.474 ------------------------------------------------------------------------------- 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 423 VAL Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 455 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 749 MET Chi-restraints excluded: chain A residue 842 THR Chi-restraints excluded: chain A residue 891 VAL Chi-restraints excluded: chain B residue 423 VAL 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 751 CYS Chi-restraints excluded: chain B residue 842 THR 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 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 817 VAL Chi-restraints excluded: chain C residue 842 THR Chi-restraints excluded: chain C residue 891 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 127 optimal weight: 2.9990 chunk 176 optimal weight: 0.9980 chunk 170 optimal weight: 3.9990 chunk 194 optimal weight: 2.9990 chunk 17 optimal weight: 0.6980 chunk 8 optimal weight: 5.9990 chunk 191 optimal weight: 0.5980 chunk 184 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 chunk 85 optimal weight: 0.7980 chunk 89 optimal weight: 0.3980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 513 HIS ** A 898 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 998 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 = 0.3966 r_free = 0.3966 target = 0.192764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.144890 restraints weight = 21479.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.141715 restraints weight = 18726.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.143346 restraints weight = 22207.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.143730 restraints weight = 13354.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.146260 restraints weight = 12121.317| |-----------------------------------------------------------------------------| r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.2532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18192 Z= 0.124 Angle : 0.605 9.723 24735 Z= 0.291 Chirality : 0.042 0.305 2727 Planarity : 0.004 0.034 3081 Dihedral : 4.014 20.265 2370 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.33 % Allowed : 16.08 % Favored : 81.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.18), residues: 2163 helix: 1.75 (0.16), residues: 1164 sheet: -0.67 (0.38), residues: 165 loop : -1.15 (0.20), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 565 TYR 0.018 0.001 TYR A 621 PHE 0.011 0.001 PHE B 397 TRP 0.019 0.001 TRP C 784 HIS 0.004 0.001 HIS B 514 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.12 (18186) covalent geometry : angle 0.60297 / 0.29 (24717) hydrogen bonds : bond 0.03298 / 2.19 ( 854) hydrogen bonds : angle 3.74399 / 2.74 ( 2535) link_BETA1-4 : bond 0.00136 / 0.09 ( 6) link_BETA1-4 : angle 1.96436 / 1.19 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2820.30 seconds wall clock time: 49 minutes 37.69 seconds (2977.69 seconds total)