Starting phenix.real_space_refine on Sat Aug 8 15:21:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vnb_65206/08_2026/9vnb_65206.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vnb_65206/08_2026/9vnb_65206.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.81 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9vnb_65206/08_2026/9vnb_65206.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vnb_65206/08_2026/9vnb_65206.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9vnb_65206/08_2026/9vnb_65206.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vnb_65206/08_2026/9vnb_65206.map" } resolution = 2.81 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= 0.001 sd= 0.011 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 4 9.91 5 S 128 5.16 5 C 18388 2.51 5 N 4636 2.21 5 O 5052 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 128 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 28208 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 7023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 873, 7023 Classifications: {'peptide': 873} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 20, 'TRANS': 852} Chain breaks: 10 Unresolved non-hydrogen bonds: 111 Unresolved non-hydrogen angles: 136 Unresolved non-hydrogen dihedrals: 88 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ARG:plan': 5, 'PHE:plan': 1, 'ASN:plan1': 4, 'GLU:plan': 3, 'ASP:plan': 3, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 66 Chain: "A" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 29 Unusual residues: {' CA': 1, 'CLR': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Restraints were copied for chains: D, C, B Time building chain proxies: 7.01, per 1000 atoms: 0.25 Number of scatterers: 28208 At special positions: 0 Unit cell: (134.792, 134.792, 153.384, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 4 19.99 S 128 16.00 O 5052 8.00 N 4636 7.00 C 18388 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 929 " - pdb=" SG CYS A 940 " distance=2.03 Simple disulfide: pdb=" SG CYS D 929 " - pdb=" SG CYS D 940 " distance=2.03 Simple disulfide: pdb=" SG CYS C 929 " - pdb=" SG CYS C 940 " distance=2.03 Simple disulfide: pdb=" SG CYS B 929 " - pdb=" SG CYS B 940 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.76 Conformation dependent library (CDL) restraints added in 1.1 seconds 6808 Ramachandran restraints generated. 3404 Oldfield, 0 Emsley, 3404 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6656 Finding SS restraints... Secondary structure from input PDB file: 180 helices and 8 sheets defined 74.2% alpha, 2.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.89 Creating SS restraints... Processing helix chain 'A' and resid 125 through 136 removed outlier: 3.596A pdb=" N LEU A 129 " --> pdb=" O ASP A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 176 Processing helix chain 'A' and resid 187 through 202 Processing helix chain 'A' and resid 216 through 220 Processing helix chain 'A' and resid 274 through 288 Processing helix chain 'A' and resid 292 through 296 removed outlier: 3.682A pdb=" N GLY A 296 " --> pdb=" O SER A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 322 Processing helix chain 'A' and resid 333 through 343 Processing helix chain 'A' and resid 351 through 362 Processing helix chain 'A' and resid 362 through 369 Processing helix chain 'A' and resid 370 through 387 removed outlier: 3.926A pdb=" N SER A 387 " --> pdb=" O GLU A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 419 removed outlier: 3.533A pdb=" N ASN A 419 " --> pdb=" O ALA A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 436 Processing helix chain 'A' and resid 438 through 446 Processing helix chain 'A' and resid 455 through 469 removed outlier: 3.547A pdb=" N GLN A 459 " --> pdb=" O SER A 455 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N GLU A 460 " --> pdb=" O ALA A 456 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N VAL A 461 " --> pdb=" O ASP A 457 " (cutoff:3.500A) Processing helix chain 'A' and resid 470 through 480 Processing helix chain 'A' and resid 483 through 488 Processing helix chain 'A' and resid 489 through 499 Processing helix chain 'A' and resid 502 through 516 Processing helix chain 'A' and resid 518 through 532 removed outlier: 3.541A pdb=" N PHE A 531 " --> pdb=" O LEU A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 571 Processing helix chain 'A' and resid 573 through 582 Processing helix chain 'A' and resid 586 through 604 removed outlier: 3.816A pdb=" N VAL A 604 " --> pdb=" O THR A 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 615 through 636 removed outlier: 3.589A pdb=" N ASN A 619 " --> pdb=" O GLU A 615 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLU A 622 " --> pdb=" O ALA A 618 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU A 631 " --> pdb=" O GLU A 627 " (cutoff:3.500A) Processing helix chain 'A' and resid 636 through 646 Processing helix chain 'A' and resid 655 through 664 Processing helix chain 'A' and resid 665 through 670 Processing helix chain 'A' and resid 671 through 684 Processing helix chain 'A' and resid 691 through 699 Processing helix chain 'A' and resid 723 through 732 Processing helix chain 'A' and resid 733 through 759 Processing helix chain 'A' and resid 765 through 790 Processing helix chain 'A' and resid 791 through 796 removed outlier: 3.619A pdb=" N ASP A 796 " --> pdb=" O ASN A 792 " (cutoff:3.500A) Processing helix chain 'A' and resid 796 through 817 Processing helix chain 'A' and resid 821 through 841 removed outlier: 3.518A pdb=" N LEU A 825 " --> pdb=" O ASN A 821 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILE A 838 " --> pdb=" O LEU A 834 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU A 841 " --> pdb=" O ILE A 837 " (cutoff:3.500A) Processing helix chain 'A' and resid 841 through 847 removed outlier: 4.378A pdb=" N HIS A 845 " --> pdb=" O LEU A 841 " (cutoff:3.500A) Processing helix chain 'A' and resid 853 through 860 Processing helix chain 'A' and resid 863 through 890 Processing helix chain 'A' and resid 895 through 904 Processing helix chain 'A' and resid 904 through 910 Processing helix chain 'A' and resid 911 through 913 No H-bonds generated for 'chain 'A' and resid 911 through 913' Processing helix chain 'A' and resid 952 through 969 Proline residue: A 958 - end of helix removed outlier: 3.612A pdb=" N ILE A 969 " --> pdb=" O LEU A 965 " (cutoff:3.500A) Processing helix chain 'A' and resid 969 through 1008 removed outlier: 5.528A pdb=" N GLU A 988 " --> pdb=" O GLY A 984 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N ASN A 989 " --> pdb=" O ILE A 985 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N PHE A1000 " --> pdb=" O PHE A 996 " (cutoff:3.500A) Processing helix chain 'A' and resid 1048 through 1073 removed outlier: 3.717A pdb=" N THR A1052 " --> pdb=" O GLU A1048 " (cutoff:3.500A) Processing helix chain 'A' and resid 1076 through 1104 Processing helix chain 'D' and resid 125 through 136 removed outlier: 3.596A pdb=" N LEU D 129 " --> pdb=" O ASP D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 158 through 176 Processing helix chain 'D' and resid 187 through 202 Processing helix chain 'D' and resid 216 through 220 Processing helix chain 'D' and resid 274 through 288 Processing helix chain 'D' and resid 292 through 296 removed outlier: 3.682A pdb=" N GLY D 296 " --> pdb=" O SER D 293 " (cutoff:3.500A) Processing helix chain 'D' and resid 309 through 322 Processing helix chain 'D' and resid 333 through 343 Processing helix chain 'D' and resid 351 through 362 Processing helix chain 'D' and resid 362 through 369 Processing helix chain 'D' and resid 370 through 387 removed outlier: 3.926A pdb=" N SER D 387 " --> pdb=" O GLU D 383 " (cutoff:3.500A) Processing helix chain 'D' and resid 402 through 419 removed outlier: 3.533A pdb=" N ASN D 419 " --> pdb=" O ALA D 415 " (cutoff:3.500A) Processing helix chain 'D' and resid 426 through 436 Processing helix chain 'D' and resid 438 through 446 Processing helix chain 'D' and resid 455 through 469 removed outlier: 3.548A pdb=" N GLN D 459 " --> pdb=" O SER D 455 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N GLU D 460 " --> pdb=" O ALA D 456 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N VAL D 461 " --> pdb=" O ASP D 457 " (cutoff:3.500A) Processing helix chain 'D' and resid 470 through 480 Processing helix chain 'D' and resid 483 through 488 Processing helix chain 'D' and resid 489 through 499 Processing helix chain 'D' and resid 502 through 516 Processing helix chain 'D' and resid 518 through 532 removed outlier: 3.541A pdb=" N PHE D 531 " --> pdb=" O LEU D 527 " (cutoff:3.500A) Processing helix chain 'D' and resid 559 through 571 Processing helix chain 'D' and resid 573 through 582 Processing helix chain 'D' and resid 586 through 604 removed outlier: 3.815A pdb=" N VAL D 604 " --> pdb=" O THR D 600 " (cutoff:3.500A) Processing helix chain 'D' and resid 615 through 636 removed outlier: 3.589A pdb=" N ASN D 619 " --> pdb=" O GLU D 615 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLU D 622 " --> pdb=" O ALA D 618 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLU D 631 " --> pdb=" O GLU D 627 " (cutoff:3.500A) Processing helix chain 'D' and resid 636 through 646 Processing helix chain 'D' and resid 655 through 664 Processing helix chain 'D' and resid 665 through 670 Processing helix chain 'D' and resid 671 through 684 Processing helix chain 'D' and resid 691 through 699 Processing helix chain 'D' and resid 723 through 732 Processing helix chain 'D' and resid 733 through 759 Processing helix chain 'D' and resid 765 through 790 Processing helix chain 'D' and resid 791 through 796 removed outlier: 3.619A pdb=" N ASP D 796 " --> pdb=" O ASN D 792 " (cutoff:3.500A) Processing helix chain 'D' and resid 796 through 817 Processing helix chain 'D' and resid 821 through 841 removed outlier: 3.519A pdb=" N LEU D 825 " --> pdb=" O ASN D 821 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILE D 838 " --> pdb=" O LEU D 834 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU D 841 " --> pdb=" O ILE D 837 " (cutoff:3.500A) Processing helix chain 'D' and resid 841 through 847 removed outlier: 4.378A pdb=" N HIS D 845 " --> pdb=" O LEU D 841 " (cutoff:3.500A) Processing helix chain 'D' and resid 853 through 860 Processing helix chain 'D' and resid 863 through 890 Processing helix chain 'D' and resid 895 through 904 Processing helix chain 'D' and resid 904 through 910 Processing helix chain 'D' and resid 911 through 913 No H-bonds generated for 'chain 'D' and resid 911 through 913' Processing helix chain 'D' and resid 952 through 969 Proline residue: D 958 - end of helix removed outlier: 3.612A pdb=" N ILE D 969 " --> pdb=" O LEU D 965 " (cutoff:3.500A) Processing helix chain 'D' and resid 969 through 1008 removed outlier: 5.529A pdb=" N GLU D 988 " --> pdb=" O GLY D 984 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N ASN D 989 " --> pdb=" O ILE D 985 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLN D 992 " --> pdb=" O GLU D 988 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N PHE D1000 " --> pdb=" O PHE D 996 " (cutoff:3.500A) Processing helix chain 'D' and resid 1048 through 1073 removed outlier: 3.718A pdb=" N THR D1052 " --> pdb=" O GLU D1048 " (cutoff:3.500A) Processing helix chain 'D' and resid 1076 through 1104 Processing helix chain 'C' and resid 125 through 136 removed outlier: 3.596A pdb=" N LEU C 129 " --> pdb=" O ASP C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 158 through 176 Processing helix chain 'C' and resid 187 through 202 Processing helix chain 'C' and resid 216 through 220 Processing helix chain 'C' and resid 274 through 288 Processing helix chain 'C' and resid 292 through 296 removed outlier: 3.683A pdb=" N GLY C 296 " --> pdb=" O SER C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 309 through 322 Processing helix chain 'C' and resid 333 through 343 Processing helix chain 'C' and resid 351 through 362 Processing helix chain 'C' and resid 362 through 369 Processing helix chain 'C' and resid 370 through 387 removed outlier: 3.925A pdb=" N SER C 387 " --> pdb=" O GLU C 383 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 419 removed outlier: 3.533A pdb=" N ASN C 419 " --> pdb=" O ALA C 415 " (cutoff:3.500A) Processing helix chain 'C' and resid 426 through 436 Processing helix chain 'C' and resid 438 through 446 Processing helix chain 'C' and resid 455 through 469 removed outlier: 3.548A pdb=" N GLN C 459 " --> pdb=" O SER C 455 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N GLU C 460 " --> pdb=" O ALA C 456 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N VAL C 461 " --> pdb=" O ASP C 457 " (cutoff:3.500A) Processing helix chain 'C' and resid 470 through 480 Processing helix chain 'C' and resid 483 through 488 Processing helix chain 'C' and resid 489 through 499 Processing helix chain 'C' and resid 502 through 516 Processing helix chain 'C' and resid 518 through 532 removed outlier: 3.542A pdb=" N PHE C 531 " --> pdb=" O LEU C 527 " (cutoff:3.500A) Processing helix chain 'C' and resid 559 through 571 Processing helix chain 'C' and resid 573 through 582 Processing helix chain 'C' and resid 586 through 604 removed outlier: 3.815A pdb=" N VAL C 604 " --> pdb=" O THR C 600 " (cutoff:3.500A) Processing helix chain 'C' and resid 615 through 636 removed outlier: 3.589A pdb=" N ASN C 619 " --> pdb=" O GLU C 615 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLU C 622 " --> pdb=" O ALA C 618 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU C 631 " --> pdb=" O GLU C 627 " (cutoff:3.500A) Processing helix chain 'C' and resid 636 through 646 Processing helix chain 'C' and resid 655 through 664 Processing helix chain 'C' and resid 665 through 670 Processing helix chain 'C' and resid 671 through 684 Processing helix chain 'C' and resid 691 through 699 Processing helix chain 'C' and resid 723 through 732 Processing helix chain 'C' and resid 733 through 759 Processing helix chain 'C' and resid 765 through 790 Processing helix chain 'C' and resid 791 through 796 removed outlier: 3.620A pdb=" N ASP C 796 " --> pdb=" O ASN C 792 " (cutoff:3.500A) Processing helix chain 'C' and resid 796 through 817 Processing helix chain 'C' and resid 821 through 841 removed outlier: 3.518A pdb=" N LEU C 825 " --> pdb=" O ASN C 821 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILE C 838 " --> pdb=" O LEU C 834 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU C 841 " --> pdb=" O ILE C 837 " (cutoff:3.500A) Processing helix chain 'C' and resid 841 through 847 removed outlier: 4.378A pdb=" N HIS C 845 " --> pdb=" O LEU C 841 " (cutoff:3.500A) Processing helix chain 'C' and resid 853 through 860 Processing helix chain 'C' and resid 863 through 890 Processing helix chain 'C' and resid 895 through 904 Processing helix chain 'C' and resid 904 through 910 Processing helix chain 'C' and resid 911 through 913 No H-bonds generated for 'chain 'C' and resid 911 through 913' Processing helix chain 'C' and resid 952 through 969 Proline residue: C 958 - end of helix removed outlier: 3.612A pdb=" N ILE C 969 " --> pdb=" O LEU C 965 " (cutoff:3.500A) Processing helix chain 'C' and resid 969 through 1008 removed outlier: 5.528A pdb=" N GLU C 988 " --> pdb=" O GLY C 984 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N ASN C 989 " --> pdb=" O ILE C 985 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N PHE C1000 " --> pdb=" O PHE C 996 " (cutoff:3.500A) Processing helix chain 'C' and resid 1048 through 1073 removed outlier: 3.717A pdb=" N THR C1052 " --> pdb=" O GLU C1048 " (cutoff:3.500A) Processing helix chain 'C' and resid 1076 through 1104 Processing helix chain 'B' and resid 125 through 136 removed outlier: 3.596A pdb=" N LEU B 129 " --> pdb=" O ASP B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 176 Processing helix chain 'B' and resid 187 through 202 Processing helix chain 'B' and resid 216 through 220 Processing helix chain 'B' and resid 274 through 288 Processing helix chain 'B' and resid 292 through 296 removed outlier: 3.681A pdb=" N GLY B 296 " --> pdb=" O SER B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 322 Processing helix chain 'B' and resid 333 through 343 Processing helix chain 'B' and resid 351 through 362 Processing helix chain 'B' and resid 362 through 369 Processing helix chain 'B' and resid 370 through 387 removed outlier: 3.926A pdb=" N SER B 387 " --> pdb=" O GLU B 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 419 removed outlier: 3.533A pdb=" N ASN B 419 " --> pdb=" O ALA B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 436 Processing helix chain 'B' and resid 438 through 446 Processing helix chain 'B' and resid 455 through 469 removed outlier: 3.548A pdb=" N GLN B 459 " --> pdb=" O SER B 455 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N GLU B 460 " --> pdb=" O ALA B 456 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N VAL B 461 " --> pdb=" O ASP B 457 " (cutoff:3.500A) Processing helix chain 'B' and resid 470 through 480 Processing helix chain 'B' and resid 483 through 488 Processing helix chain 'B' and resid 489 through 499 Processing helix chain 'B' and resid 502 through 516 Processing helix chain 'B' and resid 518 through 532 removed outlier: 3.540A pdb=" N PHE B 531 " --> pdb=" O LEU B 527 " (cutoff:3.500A) Processing helix chain 'B' and resid 559 through 571 Processing helix chain 'B' and resid 573 through 582 Processing helix chain 'B' and resid 586 through 604 removed outlier: 3.815A pdb=" N VAL B 604 " --> pdb=" O THR B 600 " (cutoff:3.500A) Processing helix chain 'B' and resid 615 through 636 removed outlier: 3.589A pdb=" N ASN B 619 " --> pdb=" O GLU B 615 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLU B 622 " --> pdb=" O ALA B 618 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLU B 631 " --> pdb=" O GLU B 627 " (cutoff:3.500A) Processing helix chain 'B' and resid 636 through 646 Processing helix chain 'B' and resid 655 through 664 Processing helix chain 'B' and resid 665 through 670 Processing helix chain 'B' and resid 671 through 684 Processing helix chain 'B' and resid 691 through 699 Processing helix chain 'B' and resid 723 through 732 Processing helix chain 'B' and resid 733 through 759 Processing helix chain 'B' and resid 765 through 790 Processing helix chain 'B' and resid 791 through 796 removed outlier: 3.619A pdb=" N ASP B 796 " --> pdb=" O ASN B 792 " (cutoff:3.500A) Processing helix chain 'B' and resid 796 through 817 Processing helix chain 'B' and resid 821 through 841 removed outlier: 3.518A pdb=" N LEU B 825 " --> pdb=" O ASN B 821 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILE B 838 " --> pdb=" O LEU B 834 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU B 841 " --> pdb=" O ILE B 837 " (cutoff:3.500A) Processing helix chain 'B' and resid 841 through 847 removed outlier: 4.378A pdb=" N HIS B 845 " --> pdb=" O LEU B 841 " (cutoff:3.500A) Processing helix chain 'B' and resid 853 through 860 Processing helix chain 'B' and resid 863 through 890 Processing helix chain 'B' and resid 895 through 904 Processing helix chain 'B' and resid 904 through 910 Processing helix chain 'B' and resid 911 through 913 No H-bonds generated for 'chain 'B' and resid 911 through 913' Processing helix chain 'B' and resid 952 through 969 Proline residue: B 958 - end of helix removed outlier: 3.612A pdb=" N ILE B 969 " --> pdb=" O LEU B 965 " (cutoff:3.500A) Processing helix chain 'B' and resid 969 through 1008 removed outlier: 5.528A pdb=" N GLU B 988 " --> pdb=" O GLY B 984 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N ASN B 989 " --> pdb=" O ILE B 985 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N PHE B1000 " --> pdb=" O PHE B 996 " (cutoff:3.500A) Processing helix chain 'B' and resid 1048 through 1073 removed outlier: 3.718A pdb=" N THR B1052 " --> pdb=" O GLU B1048 " (cutoff:3.500A) Processing helix chain 'B' and resid 1076 through 1104 Processing sheet with id=AA1, first strand: chain 'A' and resid 118 through 120 removed outlier: 3.822A pdb=" N LEU A 118 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N GLY A 213 " --> pdb=" O LEU A 261 " (cutoff:3.500A) removed outlier: 8.424A pdb=" N VAL A 263 " --> pdb=" O GLY A 213 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 178 through 180 removed outlier: 7.055A pdb=" N VAL A 145 " --> pdb=" O LEU A 180 " (cutoff:3.500A) removed outlier: 8.560A pdb=" N VAL A 327 " --> pdb=" O ILE A 301 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N CYS A 303 " --> pdb=" O VAL A 327 " (cutoff:3.500A) removed outlier: 8.251A pdb=" N VAL A 329 " --> pdb=" O CYS A 303 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 118 through 120 removed outlier: 3.822A pdb=" N LEU D 118 " --> pdb=" O LEU D 260 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N GLY D 213 " --> pdb=" O LEU D 261 " (cutoff:3.500A) removed outlier: 8.424A pdb=" N VAL D 263 " --> pdb=" O GLY D 213 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 178 through 180 removed outlier: 7.055A pdb=" N VAL D 145 " --> pdb=" O LEU D 180 " (cutoff:3.500A) removed outlier: 8.560A pdb=" N VAL D 327 " --> pdb=" O ILE D 301 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N CYS D 303 " --> pdb=" O VAL D 327 " (cutoff:3.500A) removed outlier: 8.251A pdb=" N VAL D 329 " --> pdb=" O CYS D 303 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 118 through 120 removed outlier: 3.822A pdb=" N LEU C 118 " --> pdb=" O LEU C 260 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N GLY C 213 " --> pdb=" O LEU C 261 " (cutoff:3.500A) removed outlier: 8.425A pdb=" N VAL C 263 " --> pdb=" O GLY C 213 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 178 through 180 removed outlier: 7.055A pdb=" N VAL C 145 " --> pdb=" O LEU C 180 " (cutoff:3.500A) removed outlier: 8.560A pdb=" N VAL C 327 " --> pdb=" O ILE C 301 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N CYS C 303 " --> pdb=" O VAL C 327 " (cutoff:3.500A) removed outlier: 8.251A pdb=" N VAL C 329 " --> pdb=" O CYS C 303 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 118 through 120 removed outlier: 3.821A pdb=" N LEU B 118 " --> pdb=" O LEU B 260 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N GLY B 213 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 8.425A pdb=" N VAL B 263 " --> pdb=" O GLY B 213 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 178 through 180 removed outlier: 7.054A pdb=" N VAL B 145 " --> pdb=" O LEU B 180 " (cutoff:3.500A) removed outlier: 8.560A pdb=" N VAL B 327 " --> pdb=" O ILE B 301 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N CYS B 303 " --> pdb=" O VAL B 327 " (cutoff:3.500A) removed outlier: 8.251A pdb=" N VAL B 329 " --> pdb=" O CYS B 303 " (cutoff:3.500A) 1812 hydrogen bonds defined for protein. 5400 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: 5.27 Time building geometry restraints manager: 2.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8726 1.34 - 1.46: 4550 1.46 - 1.58: 15392 1.58 - 1.69: 0 1.69 - 1.81: 196 Bond restraints: 28864 Sorted by residual: bond pdb=" N LYS A 937 " pdb=" CA LYS A 937 " ideal model delta sigma weight residual 1.453 1.485 -0.032 9.20e-03 1.18e+04 1.19e+01 bond pdb=" N LYS C 937 " pdb=" CA LYS C 937 " ideal model delta sigma weight residual 1.453 1.485 -0.031 9.20e-03 1.18e+04 1.17e+01 bond pdb=" N LYS B 937 " pdb=" CA LYS B 937 " ideal model delta sigma weight residual 1.453 1.485 -0.031 9.20e-03 1.18e+04 1.16e+01 bond pdb=" N LYS D 937 " pdb=" CA LYS D 937 " ideal model delta sigma weight residual 1.453 1.485 -0.031 9.20e-03 1.18e+04 1.16e+01 bond pdb=" N VAL D 328 " pdb=" CA VAL D 328 " ideal model delta sigma weight residual 1.455 1.494 -0.039 1.18e-02 7.18e+03 1.09e+01 ... (remaining 28859 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.39: 37181 1.39 - 2.78: 1534 2.78 - 4.16: 376 4.16 - 5.55: 81 5.55 - 6.94: 8 Bond angle restraints: 39180 Sorted by residual: angle pdb=" CA VAL B 328 " pdb=" C VAL B 328 " pdb=" O VAL B 328 " ideal model delta sigma weight residual 121.67 117.52 4.15 1.06e+00 8.90e-01 1.54e+01 angle pdb=" CA GLU D 942 " pdb=" C GLU D 942 " pdb=" O GLU D 942 " ideal model delta sigma weight residual 121.55 117.43 4.12 1.06e+00 8.90e-01 1.51e+01 angle pdb=" CA VAL A 328 " pdb=" C VAL A 328 " pdb=" O VAL A 328 " ideal model delta sigma weight residual 121.67 117.55 4.12 1.06e+00 8.90e-01 1.51e+01 angle pdb=" CA VAL D 328 " pdb=" C VAL D 328 " pdb=" O VAL D 328 " ideal model delta sigma weight residual 121.67 117.55 4.12 1.06e+00 8.90e-01 1.51e+01 angle pdb=" CA GLU B 942 " pdb=" C GLU B 942 " pdb=" O GLU B 942 " ideal model delta sigma weight residual 121.55 117.45 4.10 1.06e+00 8.90e-01 1.49e+01 ... (remaining 39175 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.62: 14753 17.62 - 35.25: 1744 35.25 - 52.87: 446 52.87 - 70.50: 105 70.50 - 88.12: 28 Dihedral angle restraints: 17076 sinusoidal: 6832 harmonic: 10244 Sorted by residual: dihedral pdb=" CA VAL C 915 " pdb=" C VAL C 915 " pdb=" N PRO C 916 " pdb=" CA PRO C 916 " ideal model delta harmonic sigma weight residual -180.00 -162.74 -17.26 0 5.00e+00 4.00e-02 1.19e+01 dihedral pdb=" CA VAL A 915 " pdb=" C VAL A 915 " pdb=" N PRO A 916 " pdb=" CA PRO A 916 " ideal model delta harmonic sigma weight residual -180.00 -162.78 -17.22 0 5.00e+00 4.00e-02 1.19e+01 dihedral pdb=" CA VAL D 915 " pdb=" C VAL D 915 " pdb=" N PRO D 916 " pdb=" CA PRO D 916 " ideal model delta harmonic sigma weight residual -180.00 -162.78 -17.22 0 5.00e+00 4.00e-02 1.19e+01 ... (remaining 17073 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 3384 0.039 - 0.078: 765 0.078 - 0.117: 219 0.117 - 0.156: 67 0.156 - 0.195: 21 Chirality restraints: 4456 Sorted by residual: chirality pdb=" CA VAL A 338 " pdb=" N VAL A 338 " pdb=" C VAL A 338 " pdb=" CB VAL A 338 " both_signs ideal model delta sigma weight residual False 2.44 2.64 -0.19 2.00e-01 2.50e+01 9.49e-01 chirality pdb=" CA VAL C 338 " pdb=" N VAL C 338 " pdb=" C VAL C 338 " pdb=" CB VAL C 338 " both_signs ideal model delta sigma weight residual False 2.44 2.64 -0.19 2.00e-01 2.50e+01 9.49e-01 chirality pdb=" CA VAL B 338 " pdb=" N VAL B 338 " pdb=" C VAL B 338 " pdb=" CB VAL B 338 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.19 2.00e-01 2.50e+01 9.27e-01 ... (remaining 4453 not shown) Planarity restraints: 4844 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 507 " 0.173 9.50e-02 1.11e+02 7.75e-02 3.89e+00 pdb=" NE ARG C 507 " -0.013 2.00e-02 2.50e+03 pdb=" CZ ARG C 507 " 0.006 2.00e-02 2.50e+03 pdb=" NH1 ARG C 507 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG C 507 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 507 " -0.172 9.50e-02 1.11e+02 7.72e-02 3.87e+00 pdb=" NE ARG A 507 " 0.013 2.00e-02 2.50e+03 pdb=" CZ ARG A 507 " -0.006 2.00e-02 2.50e+03 pdb=" NH1 ARG A 507 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A 507 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 507 " 0.172 9.50e-02 1.11e+02 7.71e-02 3.86e+00 pdb=" NE ARG B 507 " -0.013 2.00e-02 2.50e+03 pdb=" CZ ARG B 507 " 0.006 2.00e-02 2.50e+03 pdb=" NH1 ARG B 507 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG B 507 " 0.004 2.00e-02 2.50e+03 ... (remaining 4841 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 7440 2.81 - 3.33: 28733 3.33 - 3.86: 46243 3.86 - 4.38: 51879 4.38 - 4.90: 89071 Nonbonded interactions: 223366 Sorted by model distance: nonbonded pdb=" O TRP D 798 " pdb=" OD1 ASP D 802 " model vdw 2.289 3.040 nonbonded pdb=" O TRP A 798 " pdb=" OD1 ASP A 802 " model vdw 2.289 3.040 nonbonded pdb=" O TRP B 798 " pdb=" OD1 ASP B 802 " model vdw 2.289 3.040 nonbonded pdb=" O TRP C 798 " pdb=" OD1 ASP C 802 " model vdw 2.289 3.040 nonbonded pdb=" O GLU C 435 " pdb=" OE1 GLU C 435 " model vdw 2.515 3.040 ... (remaining 223361 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: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' selection = chain 'C' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.780 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: 0.030 Extract box with map and model: 0.530 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 23.670 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 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 : 0.004 0.053 28868 Z= 0.262 Angle : 0.682 6.942 39188 Z= 0.429 Chirality : 0.040 0.195 4456 Planarity : 0.004 0.077 4844 Dihedral : 16.617 88.119 10408 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.23 % Allowed : 19.83 % Favored : 78.95 % 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: 1.87 (0.14), residues: 3404 helix: 2.12 (0.11), residues: 2432 sheet: -1.58 (0.39), residues: 168 loop : -0.88 (0.20), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 162 TYR 0.019 0.001 TYR A 787 PHE 0.014 0.001 PHE B 752 TRP 0.024 0.002 TRP D 786 HIS 0.005 0.001 HIS B 946 Details of bonding type rmsd/Z covalent geometry : bond 0.00418 / 0.26 (28864) covalent geometry : angle 0.68249 / 0.43 (39180) SS BOND : bond 0.00044 / 0.02 ( 4) SS BOND : angle 0.11636 / 0.08 ( 8) hydrogen bonds : bond 0.11940 / 7.70 ( 1812) hydrogen bonds : angle 4.89152 / 3.51 ( 5400) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6808 Ramachandran restraints generated. 3404 Oldfield, 0 Emsley, 3404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6808 Ramachandran restraints generated. 3404 Oldfield, 0 Emsley, 3404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 355 time to evaluate : 1.074 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 186 TYR cc_start: 0.7967 (m-80) cc_final: 0.7560 (m-80) REVERT: A 202 SER cc_start: 0.6904 (t) cc_final: 0.6449 (p) REVERT: A 219 MET cc_start: 0.7374 (tpp) cc_final: 0.7007 (tpt) REVERT: A 398 GLU cc_start: 0.6132 (tp30) cc_final: 0.5749 (pm20) REVERT: A 877 TRP cc_start: 0.7367 (m100) cc_final: 0.6863 (m-10) REVERT: A 897 ARG cc_start: 0.7183 (mmp-170) cc_final: 0.6310 (mtm-85) REVERT: A 920 ASP cc_start: 0.7834 (m-30) cc_final: 0.7571 (m-30) REVERT: A 928 HIS cc_start: 0.4497 (m90) cc_final: 0.3911 (t-90) REVERT: A 1059 MET cc_start: 0.8351 (mmm) cc_final: 0.7808 (mmm) REVERT: D 186 TYR cc_start: 0.7879 (m-80) cc_final: 0.7417 (m-80) REVERT: D 191 TYR cc_start: 0.8100 (t80) cc_final: 0.7860 (t80) REVERT: D 202 SER cc_start: 0.6738 (t) cc_final: 0.6274 (p) REVERT: D 219 MET cc_start: 0.7436 (tpp) cc_final: 0.6999 (tpt) REVERT: D 378 ILE cc_start: 0.7153 (OUTLIER) cc_final: 0.6909 (tt) REVERT: D 398 GLU cc_start: 0.6142 (tp30) cc_final: 0.5728 (pm20) REVERT: D 575 GLU cc_start: 0.7858 (mp0) cc_final: 0.7294 (mm-30) REVERT: D 877 TRP cc_start: 0.7387 (m100) cc_final: 0.6875 (m-10) REVERT: D 897 ARG cc_start: 0.7119 (mmp-170) cc_final: 0.6200 (mtm110) REVERT: D 920 ASP cc_start: 0.7867 (m-30) cc_final: 0.7583 (m-30) REVERT: D 928 HIS cc_start: 0.4795 (m90) cc_final: 0.4078 (t-90) REVERT: D 1059 MET cc_start: 0.8283 (mmm) cc_final: 0.7714 (mmm) REVERT: C 186 TYR cc_start: 0.7861 (m-80) cc_final: 0.7458 (m-80) REVERT: C 191 TYR cc_start: 0.8083 (t80) cc_final: 0.7843 (t80) REVERT: C 202 SER cc_start: 0.6716 (t) cc_final: 0.6259 (p) REVERT: C 219 MET cc_start: 0.7427 (tpp) cc_final: 0.7034 (tpt) REVERT: C 378 ILE cc_start: 0.7156 (OUTLIER) cc_final: 0.6908 (tt) REVERT: C 398 GLU cc_start: 0.6133 (tp30) cc_final: 0.5734 (pm20) REVERT: C 575 GLU cc_start: 0.7853 (mp0) cc_final: 0.7291 (mm-30) REVERT: C 877 TRP cc_start: 0.7387 (m100) cc_final: 0.6878 (m-10) REVERT: C 897 ARG cc_start: 0.7119 (mmp-170) cc_final: 0.6206 (mtm110) REVERT: C 928 HIS cc_start: 0.4797 (m90) cc_final: 0.4076 (t-90) REVERT: C 1059 MET cc_start: 0.8282 (mmm) cc_final: 0.7712 (mmm) REVERT: B 186 TYR cc_start: 0.7865 (m-80) cc_final: 0.7468 (m-80) REVERT: B 191 TYR cc_start: 0.8084 (t80) cc_final: 0.7844 (t80) REVERT: B 202 SER cc_start: 0.6752 (t) cc_final: 0.6281 (p) REVERT: B 219 MET cc_start: 0.7428 (tpp) cc_final: 0.7039 (tpt) REVERT: B 378 ILE cc_start: 0.7155 (OUTLIER) cc_final: 0.6913 (tt) REVERT: B 398 GLU cc_start: 0.6120 (tp30) cc_final: 0.5720 (pm20) REVERT: B 575 GLU cc_start: 0.7856 (mp0) cc_final: 0.7292 (mm-30) REVERT: B 877 TRP cc_start: 0.7384 (m100) cc_final: 0.6873 (m-10) REVERT: B 897 ARG cc_start: 0.7119 (mmp-170) cc_final: 0.6210 (mtm110) REVERT: B 928 HIS cc_start: 0.4795 (m90) cc_final: 0.4074 (t-90) REVERT: B 1059 MET cc_start: 0.8285 (mmm) cc_final: 0.7713 (mmm) outliers start: 37 outliers final: 13 residues processed: 367 average time/residue: 0.4403 time to fit residues: 197.8433 Evaluate side-chains 334 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 318 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain A residue 1065 VAL Chi-restraints excluded: chain D residue 378 ILE Chi-restraints excluded: chain D residue 446 ILE Chi-restraints excluded: chain D residue 804 LEU Chi-restraints excluded: chain D residue 1065 VAL Chi-restraints excluded: chain C residue 378 ILE Chi-restraints excluded: chain C residue 446 ILE Chi-restraints excluded: chain C residue 804 LEU Chi-restraints excluded: chain C residue 1065 VAL Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain B residue 378 ILE Chi-restraints excluded: chain B residue 446 ILE Chi-restraints excluded: chain B residue 804 LEU Chi-restraints excluded: chain B residue 1065 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 197 optimal weight: 9.9990 chunk 215 optimal weight: 0.2980 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 20.0000 chunk 248 optimal weight: 0.0070 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 0.6980 chunk 183 optimal weight: 10.0000 chunk 298 optimal weight: 30.0000 overall best weight: 1.2002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 317 ASN A 635 ASN A 671 GLN A 821 ASN ** D 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 317 ASN D 635 ASN D 671 GLN D 821 ASN ** C 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 317 ASN C 635 ASN C 671 GLN C 821 ASN ** B 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 317 ASN B 635 ASN B 671 GLN B 821 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4455 r_free = 0.4455 target = 0.205273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.151071 restraints weight = 36078.514| |-----------------------------------------------------------------------------| r_work (start): 0.3830 rms_B_bonded: 2.24 r_work: 0.3676 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3542 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.1219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 28868 Z= 0.121 Angle : 0.484 5.965 39188 Z= 0.262 Chirality : 0.038 0.151 4456 Planarity : 0.003 0.027 4844 Dihedral : 4.891 52.445 4012 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 3.28 % Allowed : 19.06 % Favored : 77.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.30 (0.14), residues: 3404 helix: 2.43 (0.10), residues: 2408 sheet: -1.15 (0.40), residues: 168 loop : -0.66 (0.20), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 162 TYR 0.015 0.001 TYR C 240 PHE 0.019 0.001 PHE A 779 TRP 0.020 0.002 TRP A 994 HIS 0.009 0.001 HIS B 389 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.12 (28864) covalent geometry : angle 0.47986 / 0.26 (39180) SS BOND : bond 0.01005 / 0.50 ( 4) SS BOND : angle 4.56624 / 3.17 ( 8) hydrogen bonds : bond 0.04884 / 3.27 ( 1812) hydrogen bonds : angle 3.99412 / 2.85 ( 5400) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6808 Ramachandran restraints generated. 3404 Oldfield, 0 Emsley, 3404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6808 Ramachandran restraints generated. 3404 Oldfield, 0 Emsley, 3404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 453 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 354 time to evaluate : 0.995 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 186 TYR cc_start: 0.7910 (m-80) cc_final: 0.7645 (m-80) REVERT: A 191 TYR cc_start: 0.8244 (t80) cc_final: 0.7998 (t80) REVERT: A 202 SER cc_start: 0.6994 (t) cc_final: 0.6553 (p) REVERT: A 214 ILE cc_start: 0.8624 (OUTLIER) cc_final: 0.8401 (tp) REVERT: A 219 MET cc_start: 0.7263 (tpp) cc_final: 0.6944 (tpt) REVERT: A 398 GLU cc_start: 0.6145 (tp30) cc_final: 0.5861 (pm20) REVERT: A 516 TYR cc_start: 0.6712 (m-80) cc_final: 0.6417 (m-80) REVERT: A 842 ARG cc_start: 0.8402 (mtp85) cc_final: 0.8141 (mtp180) REVERT: A 877 TRP cc_start: 0.7396 (m100) cc_final: 0.6801 (m-10) REVERT: A 897 ARG cc_start: 0.7332 (mmp-170) cc_final: 0.6468 (mtm-85) REVERT: A 906 GLU cc_start: 0.8579 (OUTLIER) cc_final: 0.8233 (mm-30) REVERT: A 928 HIS cc_start: 0.4697 (m90) cc_final: 0.4201 (t70) REVERT: D 186 TYR cc_start: 0.7834 (m-80) cc_final: 0.7543 (m-80) REVERT: D 191 TYR cc_start: 0.8255 (t80) cc_final: 0.8014 (t80) REVERT: D 202 SER cc_start: 0.6831 (t) cc_final: 0.6393 (p) REVERT: D 219 MET cc_start: 0.7384 (tpp) cc_final: 0.6992 (tpt) REVERT: D 280 GLN cc_start: 0.9068 (tp40) cc_final: 0.8822 (tp40) REVERT: D 337 ASP cc_start: 0.7415 (t0) cc_final: 0.7212 (m-30) REVERT: D 378 ILE cc_start: 0.7385 (OUTLIER) cc_final: 0.7059 (tt) REVERT: D 398 GLU cc_start: 0.6183 (tp30) cc_final: 0.5860 (pm20) REVERT: D 516 TYR cc_start: 0.6603 (m-80) cc_final: 0.6234 (m-80) REVERT: D 842 ARG cc_start: 0.8404 (mtp85) cc_final: 0.8055 (mtp180) REVERT: D 877 TRP cc_start: 0.7414 (m100) cc_final: 0.6847 (m-10) REVERT: D 897 ARG cc_start: 0.7247 (mmp-170) cc_final: 0.6402 (mtm110) REVERT: D 906 GLU cc_start: 0.8570 (OUTLIER) cc_final: 0.8229 (mm-30) REVERT: D 928 HIS cc_start: 0.4712 (m90) cc_final: 0.4211 (t70) REVERT: C 186 TYR cc_start: 0.7827 (m-80) cc_final: 0.7513 (m-80) REVERT: C 191 TYR cc_start: 0.8264 (t80) cc_final: 0.8020 (t80) REVERT: C 202 SER cc_start: 0.6819 (t) cc_final: 0.6385 (p) REVERT: C 219 MET cc_start: 0.7370 (tpp) cc_final: 0.6978 (tpt) REVERT: C 280 GLN cc_start: 0.9067 (tp40) cc_final: 0.8819 (tp40) REVERT: C 378 ILE cc_start: 0.7373 (OUTLIER) cc_final: 0.7052 (tt) REVERT: C 398 GLU cc_start: 0.6153 (tp30) cc_final: 0.5834 (pm20) REVERT: C 516 TYR cc_start: 0.6600 (m-80) cc_final: 0.6221 (m-80) REVERT: C 842 ARG cc_start: 0.8397 (mtp85) cc_final: 0.8044 (mtp180) REVERT: C 877 TRP cc_start: 0.7406 (m100) cc_final: 0.6846 (m-10) REVERT: C 897 ARG cc_start: 0.7240 (mmp-170) cc_final: 0.6399 (mtm110) REVERT: C 906 GLU cc_start: 0.8559 (OUTLIER) cc_final: 0.8216 (mm-30) REVERT: C 928 HIS cc_start: 0.4694 (m90) cc_final: 0.4201 (t70) REVERT: B 186 TYR cc_start: 0.7851 (m-80) cc_final: 0.7567 (m-80) REVERT: B 191 TYR cc_start: 0.8256 (t80) cc_final: 0.8010 (t80) REVERT: B 202 SER cc_start: 0.6843 (t) cc_final: 0.6409 (p) REVERT: B 219 MET cc_start: 0.7354 (tpp) cc_final: 0.6961 (tpt) REVERT: B 280 GLN cc_start: 0.9075 (tp40) cc_final: 0.8825 (tp40) REVERT: B 378 ILE cc_start: 0.7351 (OUTLIER) cc_final: 0.7024 (tt) REVERT: B 398 GLU cc_start: 0.6140 (tp30) cc_final: 0.5824 (pm20) REVERT: B 516 TYR cc_start: 0.6599 (m-80) cc_final: 0.6232 (m-80) REVERT: B 842 ARG cc_start: 0.8404 (mtp85) cc_final: 0.8056 (mtp180) REVERT: B 877 TRP cc_start: 0.7430 (m100) cc_final: 0.6843 (m-10) REVERT: B 897 ARG cc_start: 0.7249 (mmp-170) cc_final: 0.6394 (mtm110) REVERT: B 906 GLU cc_start: 0.8565 (OUTLIER) cc_final: 0.8224 (mm-30) REVERT: B 928 HIS cc_start: 0.4700 (m90) cc_final: 0.4204 (t70) outliers start: 99 outliers final: 24 residues processed: 422 average time/residue: 0.4817 time to fit residues: 244.1459 Evaluate side-chains 338 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 306 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 587 CYS Chi-restraints excluded: chain A residue 624 ARG Chi-restraints excluded: chain A residue 906 GLU Chi-restraints excluded: chain A residue 992 GLN Chi-restraints excluded: chain D residue 378 ILE Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 587 CYS Chi-restraints excluded: chain D residue 624 ARG Chi-restraints excluded: chain D residue 860 LEU Chi-restraints excluded: chain D residue 906 GLU Chi-restraints excluded: chain D residue 992 GLN Chi-restraints excluded: chain D residue 1065 VAL Chi-restraints excluded: chain C residue 378 ILE Chi-restraints excluded: chain C residue 385 LEU Chi-restraints excluded: chain C residue 587 CYS Chi-restraints excluded: chain C residue 624 ARG Chi-restraints excluded: chain C residue 860 LEU Chi-restraints excluded: chain C residue 906 GLU Chi-restraints excluded: chain C residue 992 GLN Chi-restraints excluded: chain C residue 1065 VAL Chi-restraints excluded: chain B residue 378 ILE Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 587 CYS Chi-restraints excluded: chain B residue 624 ARG Chi-restraints excluded: chain B residue 860 LEU Chi-restraints excluded: chain B residue 906 GLU Chi-restraints excluded: chain B residue 992 GLN Chi-restraints excluded: chain B residue 1004 GLU Chi-restraints excluded: chain B residue 1065 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 131 optimal weight: 9.9990 chunk 269 optimal weight: 7.9990 chunk 90 optimal weight: 9.9990 chunk 138 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 187 optimal weight: 5.9990 chunk 311 optimal weight: 2.9990 chunk 325 optimal weight: 0.9980 chunk 143 optimal weight: 6.9990 chunk 262 optimal weight: 30.0000 chunk 336 optimal weight: 3.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 671 GLN D 671 GLN C 136 HIS C 671 GLN B 136 HIS B 671 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4385 r_free = 0.4385 target = 0.195718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.139288 restraints weight = 35868.154| |-----------------------------------------------------------------------------| r_work (start): 0.3742 rms_B_bonded: 2.43 r_work: 0.3577 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3443 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.1637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 28868 Z= 0.173 Angle : 0.541 6.133 39188 Z= 0.291 Chirality : 0.040 0.146 4456 Planarity : 0.004 0.033 4844 Dihedral : 4.831 58.327 3993 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 4.81 % Allowed : 18.53 % Favored : 76.66 % 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: 2.14 (0.14), residues: 3404 helix: 2.34 (0.10), residues: 2404 sheet: -1.08 (0.40), residues: 168 loop : -0.82 (0.20), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 507 TYR 0.016 0.001 TYR D 787 PHE 0.025 0.002 PHE A 752 TRP 0.021 0.002 TRP B 786 HIS 0.007 0.001 HIS D 389 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.17 (28864) covalent geometry : angle 0.53889 / 0.29 (39180) SS BOND : bond 0.00045 / 0.02 ( 4) SS BOND : angle 3.00692 / 2.10 ( 8) hydrogen bonds : bond 0.06369 / 4.27 ( 1812) hydrogen bonds : angle 4.05514 / 2.90 ( 5400) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6808 Ramachandran restraints generated. 3404 Oldfield, 0 Emsley, 3404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6808 Ramachandran restraints generated. 3404 Oldfield, 0 Emsley, 3404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 466 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 321 time to evaluate : 0.999 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 186 TYR cc_start: 0.7896 (m-80) cc_final: 0.7612 (m-80) REVERT: A 191 TYR cc_start: 0.8252 (t80) cc_final: 0.7963 (t80) REVERT: A 202 SER cc_start: 0.7200 (t) cc_final: 0.6861 (p) REVERT: A 398 GLU cc_start: 0.6123 (tp30) cc_final: 0.5887 (pm20) REVERT: A 511 ILE cc_start: 0.7115 (mt) cc_final: 0.6786 (pp) REVERT: A 842 ARG cc_start: 0.8446 (mtp85) cc_final: 0.8171 (mtp180) REVERT: A 877 TRP cc_start: 0.7451 (m100) cc_final: 0.6801 (m-10) REVERT: A 897 ARG cc_start: 0.7458 (mmp-170) cc_final: 0.6590 (mtm-85) REVERT: A 906 GLU cc_start: 0.8680 (OUTLIER) cc_final: 0.8337 (mm-30) REVERT: A 928 HIS cc_start: 0.5025 (m90) cc_final: 0.4510 (t-170) REVERT: D 186 TYR cc_start: 0.7855 (m-80) cc_final: 0.7499 (m-80) REVERT: D 191 TYR cc_start: 0.8253 (t80) cc_final: 0.7965 (t80) REVERT: D 202 SER cc_start: 0.7183 (t) cc_final: 0.6812 (p) REVERT: D 219 MET cc_start: 0.7361 (tpp) cc_final: 0.7142 (tpt) REVERT: D 378 ILE cc_start: 0.7348 (OUTLIER) cc_final: 0.7051 (tt) REVERT: D 398 GLU cc_start: 0.6131 (tp30) cc_final: 0.5872 (pm20) REVERT: D 439 LEU cc_start: 0.7621 (OUTLIER) cc_final: 0.7322 (tp) REVERT: D 491 GLU cc_start: 0.8603 (mp0) cc_final: 0.8304 (mp0) REVERT: D 511 ILE cc_start: 0.7139 (mt) cc_final: 0.6833 (pp) REVERT: D 842 ARG cc_start: 0.8444 (mtp85) cc_final: 0.8139 (mtp180) REVERT: D 877 TRP cc_start: 0.7430 (m100) cc_final: 0.6799 (m-10) REVERT: D 897 ARG cc_start: 0.7432 (mmp-170) cc_final: 0.6565 (mtm-85) REVERT: D 906 GLU cc_start: 0.8690 (OUTLIER) cc_final: 0.8350 (mm-30) REVERT: D 928 HIS cc_start: 0.4941 (m90) cc_final: 0.4440 (t-170) REVERT: C 186 TYR cc_start: 0.7844 (m-80) cc_final: 0.7547 (m-80) REVERT: C 191 TYR cc_start: 0.8250 (t80) cc_final: 0.7973 (t80) REVERT: C 202 SER cc_start: 0.7175 (t) cc_final: 0.6806 (p) REVERT: C 219 MET cc_start: 0.7382 (tpp) cc_final: 0.7159 (tpt) REVERT: C 334 GLN cc_start: 0.6917 (OUTLIER) cc_final: 0.6709 (mp10) REVERT: C 378 ILE cc_start: 0.7341 (OUTLIER) cc_final: 0.7050 (tt) REVERT: C 398 GLU cc_start: 0.6147 (tp30) cc_final: 0.5881 (pm20) REVERT: C 439 LEU cc_start: 0.7628 (OUTLIER) cc_final: 0.7324 (tp) REVERT: C 491 GLU cc_start: 0.8612 (mp0) cc_final: 0.8284 (mp0) REVERT: C 511 ILE cc_start: 0.7142 (mt) cc_final: 0.6839 (pp) REVERT: C 575 GLU cc_start: 0.8044 (mp0) cc_final: 0.7510 (mm-30) REVERT: C 842 ARG cc_start: 0.8448 (mtp85) cc_final: 0.8141 (mtp180) REVERT: C 877 TRP cc_start: 0.7428 (m100) cc_final: 0.6802 (m-10) REVERT: C 897 ARG cc_start: 0.7431 (mmp-170) cc_final: 0.6572 (mtm-85) REVERT: C 906 GLU cc_start: 0.8692 (OUTLIER) cc_final: 0.8357 (mm-30) REVERT: C 928 HIS cc_start: 0.4935 (m90) cc_final: 0.4453 (t-170) REVERT: B 186 TYR cc_start: 0.7866 (m-80) cc_final: 0.7566 (m-80) REVERT: B 191 TYR cc_start: 0.8247 (t80) cc_final: 0.7969 (t80) REVERT: B 202 SER cc_start: 0.7189 (t) cc_final: 0.6816 (p) REVERT: B 219 MET cc_start: 0.7397 (tpp) cc_final: 0.7179 (tpt) REVERT: B 378 ILE cc_start: 0.7385 (OUTLIER) cc_final: 0.7087 (tt) REVERT: B 398 GLU cc_start: 0.6149 (tp30) cc_final: 0.5888 (pm20) REVERT: B 439 LEU cc_start: 0.7623 (OUTLIER) cc_final: 0.7315 (tp) REVERT: B 491 GLU cc_start: 0.8604 (mp0) cc_final: 0.8309 (mp0) REVERT: B 511 ILE cc_start: 0.7138 (mt) cc_final: 0.6834 (pp) REVERT: B 575 GLU cc_start: 0.8048 (mp0) cc_final: 0.7508 (mm-30) REVERT: B 842 ARG cc_start: 0.8460 (mtp85) cc_final: 0.8149 (mtp180) REVERT: B 877 TRP cc_start: 0.7433 (m100) cc_final: 0.6798 (m-10) REVERT: B 897 ARG cc_start: 0.7396 (mmp-170) cc_final: 0.6553 (mtm-85) REVERT: B 906 GLU cc_start: 0.8691 (OUTLIER) cc_final: 0.8358 (mm-30) REVERT: B 928 HIS cc_start: 0.4940 (m90) cc_final: 0.4461 (t-170) outliers start: 145 outliers final: 54 residues processed: 426 average time/residue: 0.5696 time to fit residues: 287.4949 Evaluate side-chains 356 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 291 time to evaluate : 1.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 587 CYS Chi-restraints excluded: chain A residue 624 ARG Chi-restraints excluded: chain A residue 758 MET Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain A residue 899 ILE Chi-restraints excluded: chain A residue 906 GLU Chi-restraints excluded: chain A residue 929 CYS Chi-restraints excluded: chain A residue 992 GLN Chi-restraints excluded: chain A residue 1004 GLU Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 319 SER Chi-restraints excluded: chain D residue 378 ILE Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 393 VAL Chi-restraints excluded: chain D residue 418 THR Chi-restraints excluded: chain D residue 439 LEU Chi-restraints excluded: chain D residue 587 CYS Chi-restraints excluded: chain D residue 624 ARG Chi-restraints excluded: chain D residue 758 MET Chi-restraints excluded: chain D residue 783 VAL Chi-restraints excluded: chain D residue 899 ILE Chi-restraints excluded: chain D residue 906 GLU Chi-restraints excluded: chain D residue 929 CYS Chi-restraints excluded: chain D residue 992 GLN Chi-restraints excluded: chain D residue 1004 GLU Chi-restraints excluded: chain D residue 1065 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 319 SER Chi-restraints excluded: chain C residue 334 GLN Chi-restraints excluded: chain C residue 378 ILE Chi-restraints excluded: chain C residue 385 LEU Chi-restraints excluded: chain C residue 393 VAL Chi-restraints excluded: chain C residue 418 THR Chi-restraints excluded: chain C residue 439 LEU Chi-restraints excluded: chain C residue 587 CYS Chi-restraints excluded: chain C residue 624 ARG Chi-restraints excluded: chain C residue 758 MET Chi-restraints excluded: chain C residue 783 VAL Chi-restraints excluded: chain C residue 899 ILE Chi-restraints excluded: chain C residue 906 GLU Chi-restraints excluded: chain C residue 929 CYS Chi-restraints excluded: chain C residue 992 GLN Chi-restraints excluded: chain C residue 1004 GLU Chi-restraints excluded: chain C residue 1065 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain B residue 378 ILE Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 587 CYS Chi-restraints excluded: chain B residue 624 ARG Chi-restraints excluded: chain B residue 758 MET Chi-restraints excluded: chain B residue 783 VAL Chi-restraints excluded: chain B residue 899 ILE Chi-restraints excluded: chain B residue 906 GLU Chi-restraints excluded: chain B residue 929 CYS Chi-restraints excluded: chain B residue 992 GLN Chi-restraints excluded: chain B residue 1004 GLU Chi-restraints excluded: chain B residue 1065 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 192 optimal weight: 10.0000 chunk 345 optimal weight: 7.9990 chunk 237 optimal weight: 4.9990 chunk 238 optimal weight: 2.9990 chunk 154 optimal weight: 0.7980 chunk 328 optimal weight: 2.9990 chunk 146 optimal weight: 0.0470 chunk 291 optimal weight: 10.0000 chunk 55 optimal weight: 0.9980 chunk 344 optimal weight: 5.9990 chunk 29 optimal weight: 0.9980 overall best weight: 1.1680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 136 HIS A 317 ASN A 671 GLN D 136 HIS D 317 ASN D 671 GLN C 136 HIS C 317 ASN C 671 GLN B 136 HIS B 317 ASN B 671 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.198043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.139591 restraints weight = 35552.670| |-----------------------------------------------------------------------------| r_work (start): 0.3752 rms_B_bonded: 2.61 r_work: 0.3604 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3473 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.1904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 28868 Z= 0.110 Angle : 0.457 8.889 39188 Z= 0.246 Chirality : 0.037 0.134 4456 Planarity : 0.003 0.034 4844 Dihedral : 4.498 57.894 3993 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 3.45 % Allowed : 20.42 % Favored : 76.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.39 (0.14), residues: 3404 helix: 2.54 (0.10), residues: 2408 sheet: -0.85 (0.40), residues: 172 loop : -0.84 (0.20), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 162 TYR 0.017 0.001 TYR D 787 PHE 0.013 0.001 PHE B 752 TRP 0.020 0.001 TRP D 994 HIS 0.006 0.001 HIS A 389 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.11 (28864) covalent geometry : angle 0.45537 / 0.25 (39180) SS BOND : bond 0.00006 / 0.00 ( 4) SS BOND : angle 2.49074 / 1.79 ( 8) hydrogen bonds : bond 0.04590 / 3.08 ( 1812) hydrogen bonds : angle 3.78094 / 2.69 ( 5400) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6808 Ramachandran restraints generated. 3404 Oldfield, 0 Emsley, 3404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6808 Ramachandran restraints generated. 3404 Oldfield, 0 Emsley, 3404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 309 time to evaluate : 0.937 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 186 TYR cc_start: 0.7843 (m-80) cc_final: 0.7598 (m-80) REVERT: A 191 TYR cc_start: 0.8022 (t80) cc_final: 0.7781 (t80) REVERT: A 299 ILE cc_start: 0.7511 (OUTLIER) cc_final: 0.7239 (mm) REVERT: A 511 ILE cc_start: 0.7089 (mt) cc_final: 0.6716 (pp) REVERT: A 842 ARG cc_start: 0.8360 (mtp85) cc_final: 0.8010 (mtp180) REVERT: A 877 TRP cc_start: 0.7429 (m100) cc_final: 0.6712 (m-10) REVERT: A 897 ARG cc_start: 0.7168 (mmp-170) cc_final: 0.6202 (mtm110) REVERT: A 906 GLU cc_start: 0.8672 (OUTLIER) cc_final: 0.8335 (mm-30) REVERT: A 928 HIS cc_start: 0.4796 (m90) cc_final: 0.4191 (t70) REVERT: D 171 ILE cc_start: 0.7322 (OUTLIER) cc_final: 0.7105 (mt) REVERT: D 186 TYR cc_start: 0.7834 (m-80) cc_final: 0.7509 (m-80) REVERT: D 191 TYR cc_start: 0.8044 (t80) cc_final: 0.7763 (t80) REVERT: D 511 ILE cc_start: 0.7098 (mt) cc_final: 0.6770 (pp) REVERT: D 575 GLU cc_start: 0.7836 (mp0) cc_final: 0.7312 (mm-30) REVERT: D 842 ARG cc_start: 0.8360 (mtp85) cc_final: 0.8010 (mtp180) REVERT: D 877 TRP cc_start: 0.7411 (m100) cc_final: 0.6696 (m-10) REVERT: D 897 ARG cc_start: 0.7159 (mmp-170) cc_final: 0.6183 (mtm110) REVERT: D 906 GLU cc_start: 0.8659 (OUTLIER) cc_final: 0.8322 (mm-30) REVERT: D 928 HIS cc_start: 0.4776 (m90) cc_final: 0.4139 (t70) REVERT: C 171 ILE cc_start: 0.7278 (OUTLIER) cc_final: 0.7069 (mt) REVERT: C 186 TYR cc_start: 0.7824 (m-80) cc_final: 0.7549 (m-80) REVERT: C 191 TYR cc_start: 0.8014 (t80) cc_final: 0.7778 (t80) REVERT: C 398 GLU cc_start: 0.6119 (tp30) cc_final: 0.5890 (pm20) REVERT: C 511 ILE cc_start: 0.7103 (mt) cc_final: 0.6775 (pp) REVERT: C 575 GLU cc_start: 0.7833 (mp0) cc_final: 0.7314 (mm-30) REVERT: C 842 ARG cc_start: 0.8357 (mtp85) cc_final: 0.8005 (mtp180) REVERT: C 877 TRP cc_start: 0.7417 (m100) cc_final: 0.6693 (m-10) REVERT: C 897 ARG cc_start: 0.7152 (mmp-170) cc_final: 0.6181 (mtm110) REVERT: C 906 GLU cc_start: 0.8666 (OUTLIER) cc_final: 0.8328 (mm-30) REVERT: C 928 HIS cc_start: 0.4786 (m90) cc_final: 0.4135 (t70) REVERT: B 171 ILE cc_start: 0.7290 (OUTLIER) cc_final: 0.7077 (mt) REVERT: B 186 TYR cc_start: 0.7833 (m-80) cc_final: 0.7557 (m-80) REVERT: B 191 TYR cc_start: 0.8004 (t80) cc_final: 0.7764 (t80) REVERT: B 398 GLU cc_start: 0.6122 (tp30) cc_final: 0.5888 (pm20) REVERT: B 511 ILE cc_start: 0.7098 (mt) cc_final: 0.6772 (pp) REVERT: B 575 GLU cc_start: 0.7834 (mp0) cc_final: 0.7312 (mm-30) REVERT: B 842 ARG cc_start: 0.8357 (mtp85) cc_final: 0.8002 (mtp180) REVERT: B 877 TRP cc_start: 0.7423 (m100) cc_final: 0.6706 (m-10) REVERT: B 897 ARG cc_start: 0.7151 (mmp-170) cc_final: 0.6181 (mtm110) REVERT: B 906 GLU cc_start: 0.8668 (OUTLIER) cc_final: 0.8330 (mm-30) REVERT: B 928 HIS cc_start: 0.4783 (m90) cc_final: 0.4137 (t70) outliers start: 104 outliers final: 41 residues processed: 390 average time/residue: 0.5758 time to fit residues: 265.1564 Evaluate side-chains 339 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 290 time to evaluate : 1.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 587 CYS Chi-restraints excluded: chain A residue 624 ARG Chi-restraints excluded: chain A residue 686 ILE Chi-restraints excluded: chain A residue 758 MET Chi-restraints excluded: chain A residue 899 ILE Chi-restraints excluded: chain A residue 906 GLU Chi-restraints excluded: chain A residue 929 CYS Chi-restraints excluded: chain A residue 992 GLN Chi-restraints excluded: chain A residue 1004 GLU Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 393 VAL Chi-restraints excluded: chain D residue 587 CYS Chi-restraints excluded: chain D residue 624 ARG Chi-restraints excluded: chain D residue 686 ILE Chi-restraints excluded: chain D residue 758 MET Chi-restraints excluded: chain D residue 899 ILE Chi-restraints excluded: chain D residue 906 GLU Chi-restraints excluded: chain D residue 929 CYS Chi-restraints excluded: chain D residue 992 GLN Chi-restraints excluded: chain D residue 1004 GLU Chi-restraints excluded: chain C residue 171 ILE Chi-restraints excluded: chain C residue 385 LEU Chi-restraints excluded: chain C residue 393 VAL Chi-restraints excluded: chain C residue 587 CYS Chi-restraints excluded: chain C residue 624 ARG Chi-restraints excluded: chain C residue 686 ILE Chi-restraints excluded: chain C residue 758 MET Chi-restraints excluded: chain C residue 899 ILE Chi-restraints excluded: chain C residue 906 GLU Chi-restraints excluded: chain C residue 929 CYS Chi-restraints excluded: chain C residue 992 GLN Chi-restraints excluded: chain C residue 1004 GLU Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 587 CYS Chi-restraints excluded: chain B residue 624 ARG Chi-restraints excluded: chain B residue 686 ILE Chi-restraints excluded: chain B residue 758 MET Chi-restraints excluded: chain B residue 899 ILE Chi-restraints excluded: chain B residue 906 GLU Chi-restraints excluded: chain B residue 929 CYS Chi-restraints excluded: chain B residue 992 GLN Chi-restraints excluded: chain B residue 1004 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 124 optimal weight: 20.0000 chunk 88 optimal weight: 30.0000 chunk 117 optimal weight: 0.9990 chunk 250 optimal weight: 0.5980 chunk 329 optimal weight: 2.9990 chunk 263 optimal weight: 9.9990 chunk 228 optimal weight: 4.9990 chunk 258 optimal weight: 4.9990 chunk 37 optimal weight: 20.0000 chunk 55 optimal weight: 5.9990 chunk 291 optimal weight: 8.9990 overall best weight: 2.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 107 GLN A 135 GLN A 671 GLN D 107 GLN D 510 GLN D 671 GLN C 107 GLN C 136 HIS C 510 GLN C 671 GLN B 107 GLN B 136 HIS B 510 GLN B 671 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4342 r_free = 0.4342 target = 0.194126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.133722 restraints weight = 35529.101| |-----------------------------------------------------------------------------| r_work (start): 0.3666 rms_B_bonded: 2.18 r_work: 0.3555 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3429 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.2085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 28868 Z= 0.171 Angle : 0.541 8.996 39188 Z= 0.288 Chirality : 0.039 0.144 4456 Planarity : 0.004 0.038 4844 Dihedral : 4.413 24.772 3984 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 4.87 % Allowed : 20.06 % Favored : 75.07 % 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: 2.17 (0.14), residues: 3404 helix: 2.37 (0.10), residues: 2404 sheet: -0.70 (0.41), residues: 168 loop : -0.93 (0.20), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 162 TYR 0.016 0.001 TYR A 787 PHE 0.023 0.002 PHE B 752 TRP 0.015 0.002 TRP D 994 HIS 0.006 0.001 HIS D 389 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.17 (28864) covalent geometry : angle 0.53947 / 0.29 (39180) SS BOND : bond 0.00028 / 0.01 ( 4) SS BOND : angle 2.63673 / 1.89 ( 8) hydrogen bonds : bond 0.06279 / 4.21 ( 1812) hydrogen bonds : angle 3.94733 / 2.82 ( 5400) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6808 Ramachandran restraints generated. 3404 Oldfield, 0 Emsley, 3404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6808 Ramachandran restraints generated. 3404 Oldfield, 0 Emsley, 3404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 304 time to evaluate : 1.059 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 186 TYR cc_start: 0.7885 (m-80) cc_final: 0.7670 (m-80) REVERT: A 191 TYR cc_start: 0.8244 (t80) cc_final: 0.7975 (t80) REVERT: A 337 ASP cc_start: 0.7479 (t0) cc_final: 0.7279 (m-30) REVERT: A 439 LEU cc_start: 0.7710 (OUTLIER) cc_final: 0.7344 (tp) REVERT: A 491 GLU cc_start: 0.8455 (mp0) cc_final: 0.8168 (mp0) REVERT: A 575 GLU cc_start: 0.7941 (mp0) cc_final: 0.7562 (mm-30) REVERT: A 842 ARG cc_start: 0.8439 (mtp85) cc_final: 0.8169 (mtp180) REVERT: A 877 TRP cc_start: 0.7431 (m100) cc_final: 0.6848 (m-10) REVERT: A 897 ARG cc_start: 0.7335 (mmp-170) cc_final: 0.6503 (mtm110) REVERT: A 906 GLU cc_start: 0.8651 (OUTLIER) cc_final: 0.8299 (mm-30) REVERT: A 928 HIS cc_start: 0.5045 (m90) cc_final: 0.4520 (t-90) REVERT: A 935 GLU cc_start: 0.7467 (OUTLIER) cc_final: 0.6960 (mt-10) REVERT: D 186 TYR cc_start: 0.7871 (m-80) cc_final: 0.7589 (m-80) REVERT: D 191 TYR cc_start: 0.8247 (t80) cc_final: 0.7973 (t80) REVERT: D 337 ASP cc_start: 0.7438 (t0) cc_final: 0.7228 (m-30) REVERT: D 378 ILE cc_start: 0.7330 (OUTLIER) cc_final: 0.7067 (tt) REVERT: D 439 LEU cc_start: 0.7696 (OUTLIER) cc_final: 0.7393 (tp) REVERT: D 491 GLU cc_start: 0.8445 (mp0) cc_final: 0.8144 (mp0) REVERT: D 511 ILE cc_start: 0.7248 (mt) cc_final: 0.6900 (pp) REVERT: D 575 GLU cc_start: 0.7999 (mp0) cc_final: 0.7589 (mm-30) REVERT: D 842 ARG cc_start: 0.8429 (mtp85) cc_final: 0.8160 (mtp180) REVERT: D 897 ARG cc_start: 0.7316 (mmp-170) cc_final: 0.6489 (mtm110) REVERT: D 906 GLU cc_start: 0.8640 (OUTLIER) cc_final: 0.8280 (mm-30) REVERT: D 928 HIS cc_start: 0.4996 (m90) cc_final: 0.4449 (t-90) REVERT: D 935 GLU cc_start: 0.7435 (OUTLIER) cc_final: 0.6915 (mt-10) REVERT: C 186 TYR cc_start: 0.7858 (m-80) cc_final: 0.7617 (m-80) REVERT: C 191 TYR cc_start: 0.8258 (t80) cc_final: 0.7972 (t80) REVERT: C 378 ILE cc_start: 0.7330 (OUTLIER) cc_final: 0.7010 (tt) REVERT: C 439 LEU cc_start: 0.7710 (OUTLIER) cc_final: 0.7408 (tp) REVERT: C 491 GLU cc_start: 0.8453 (mp0) cc_final: 0.8198 (mp0) REVERT: C 511 ILE cc_start: 0.7298 (mt) cc_final: 0.6954 (pp) REVERT: C 575 GLU cc_start: 0.7960 (mp0) cc_final: 0.7562 (mm-30) REVERT: C 842 ARG cc_start: 0.8444 (mtp85) cc_final: 0.8178 (mtp180) REVERT: C 897 ARG cc_start: 0.7323 (mmp-170) cc_final: 0.6492 (mtm110) REVERT: C 906 GLU cc_start: 0.8661 (OUTLIER) cc_final: 0.8307 (mm-30) REVERT: C 928 HIS cc_start: 0.4996 (m90) cc_final: 0.4473 (t-90) REVERT: C 935 GLU cc_start: 0.7456 (OUTLIER) cc_final: 0.6959 (mt-10) REVERT: B 186 TYR cc_start: 0.7859 (m-80) cc_final: 0.7617 (m-80) REVERT: B 191 TYR cc_start: 0.8251 (t80) cc_final: 0.7964 (t80) REVERT: B 378 ILE cc_start: 0.7316 (OUTLIER) cc_final: 0.7046 (tt) REVERT: B 439 LEU cc_start: 0.7697 (OUTLIER) cc_final: 0.7393 (tp) REVERT: B 491 GLU cc_start: 0.8453 (mp0) cc_final: 0.8147 (mp0) REVERT: B 511 ILE cc_start: 0.7267 (mt) cc_final: 0.6910 (pp) REVERT: B 575 GLU cc_start: 0.7988 (mp0) cc_final: 0.7594 (mm-30) REVERT: B 842 ARG cc_start: 0.8433 (mtp85) cc_final: 0.8168 (mtp180) REVERT: B 897 ARG cc_start: 0.7317 (mmp-170) cc_final: 0.6495 (mtm110) REVERT: B 906 GLU cc_start: 0.8641 (OUTLIER) cc_final: 0.8283 (mm-30) REVERT: B 928 HIS cc_start: 0.5006 (m90) cc_final: 0.4463 (t-90) REVERT: B 935 GLU cc_start: 0.7422 (OUTLIER) cc_final: 0.6906 (mt-10) outliers start: 147 outliers final: 61 residues processed: 419 average time/residue: 0.5860 time to fit residues: 289.4359 Evaluate side-chains 358 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 282 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 587 CYS Chi-restraints excluded: chain A residue 624 ARG Chi-restraints excluded: chain A residue 686 ILE Chi-restraints excluded: chain A residue 758 MET Chi-restraints excluded: chain A residue 899 ILE Chi-restraints excluded: chain A residue 906 GLU Chi-restraints excluded: chain A residue 929 CYS Chi-restraints excluded: chain A residue 935 GLU Chi-restraints excluded: chain A residue 941 VAL Chi-restraints excluded: chain A residue 992 GLN Chi-restraints excluded: chain A residue 1004 GLU Chi-restraints excluded: chain D residue 201 ILE Chi-restraints excluded: chain D residue 225 THR Chi-restraints excluded: chain D residue 378 ILE Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 393 VAL Chi-restraints excluded: chain D residue 439 LEU Chi-restraints excluded: chain D residue 446 ILE Chi-restraints excluded: chain D residue 587 CYS Chi-restraints excluded: chain D residue 624 ARG Chi-restraints excluded: chain D residue 686 ILE Chi-restraints excluded: chain D residue 758 MET Chi-restraints excluded: chain D residue 801 MET Chi-restraints excluded: chain D residue 899 ILE Chi-restraints excluded: chain D residue 906 GLU Chi-restraints excluded: chain D residue 929 CYS Chi-restraints excluded: chain D residue 935 GLU Chi-restraints excluded: chain D residue 941 VAL Chi-restraints excluded: chain D residue 992 GLN Chi-restraints excluded: chain D residue 1004 GLU Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 353 MET Chi-restraints excluded: chain C residue 378 ILE Chi-restraints excluded: chain C residue 385 LEU Chi-restraints excluded: chain C residue 393 VAL Chi-restraints excluded: chain C residue 439 LEU Chi-restraints excluded: chain C residue 446 ILE Chi-restraints excluded: chain C residue 587 CYS Chi-restraints excluded: chain C residue 624 ARG Chi-restraints excluded: chain C residue 686 ILE Chi-restraints excluded: chain C residue 758 MET Chi-restraints excluded: chain C residue 801 MET Chi-restraints excluded: chain C residue 899 ILE Chi-restraints excluded: chain C residue 906 GLU Chi-restraints excluded: chain C residue 929 CYS Chi-restraints excluded: chain C residue 935 GLU Chi-restraints excluded: chain C residue 941 VAL Chi-restraints excluded: chain C residue 992 GLN Chi-restraints excluded: chain C residue 1004 GLU Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 353 MET Chi-restraints excluded: chain B residue 378 ILE Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 446 ILE Chi-restraints excluded: chain B residue 587 CYS Chi-restraints excluded: chain B residue 624 ARG Chi-restraints excluded: chain B residue 686 ILE Chi-restraints excluded: chain B residue 758 MET Chi-restraints excluded: chain B residue 899 ILE Chi-restraints excluded: chain B residue 906 GLU Chi-restraints excluded: chain B residue 929 CYS Chi-restraints excluded: chain B residue 935 GLU Chi-restraints excluded: chain B residue 941 VAL Chi-restraints excluded: chain B residue 992 GLN Chi-restraints excluded: chain B residue 1004 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 111 optimal weight: 4.9990 chunk 134 optimal weight: 1.9990 chunk 81 optimal weight: 20.0000 chunk 251 optimal weight: 3.9990 chunk 140 optimal weight: 10.0000 chunk 33 optimal weight: 0.8980 chunk 265 optimal weight: 30.0000 chunk 125 optimal weight: 10.0000 chunk 37 optimal weight: 20.0000 chunk 221 optimal weight: 1.9990 chunk 228 optimal weight: 7.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 671 GLN D 135 GLN D 671 GLN C 135 GLN C 136 HIS C 671 GLN B 136 HIS B 671 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.191704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.131072 restraints weight = 35270.017| |-----------------------------------------------------------------------------| r_work (start): 0.3633 rms_B_bonded: 2.74 r_work: 0.3440 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.2355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 28868 Z= 0.164 Angle : 0.540 10.051 39188 Z= 0.285 Chirality : 0.039 0.137 4456 Planarity : 0.004 0.039 4844 Dihedral : 4.443 24.417 3984 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 4.87 % Allowed : 21.02 % Favored : 74.10 % 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: 2.07 (0.14), residues: 3404 helix: 2.31 (0.10), residues: 2404 sheet: -0.70 (0.41), residues: 168 loop : -1.06 (0.20), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 162 TYR 0.019 0.001 TYR C 787 PHE 0.020 0.002 PHE D 752 TRP 0.017 0.002 TRP C 994 HIS 0.005 0.001 HIS C 389 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.16 (28864) covalent geometry : angle 0.53860 / 0.28 (39180) SS BOND : bond 0.00077 / 0.04 ( 4) SS BOND : angle 2.76290 / 1.99 ( 8) hydrogen bonds : bond 0.05995 / 4.02 ( 1812) hydrogen bonds : angle 3.91621 / 2.79 ( 5400) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6808 Ramachandran restraints generated. 3404 Oldfield, 0 Emsley, 3404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6808 Ramachandran restraints generated. 3404 Oldfield, 0 Emsley, 3404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 290 time to evaluate : 0.976 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 398 GLU cc_start: 0.6369 (pm20) cc_final: 0.6165 (pm20) REVERT: A 439 LEU cc_start: 0.7608 (OUTLIER) cc_final: 0.7284 (tp) REVERT: A 491 GLU cc_start: 0.8543 (mp0) cc_final: 0.8181 (mp0) REVERT: A 575 GLU cc_start: 0.7799 (mp0) cc_final: 0.7319 (mm-30) REVERT: A 842 ARG cc_start: 0.8267 (mtp85) cc_final: 0.7947 (mtp180) REVERT: A 877 TRP cc_start: 0.7245 (m100) cc_final: 0.6678 (m-10) REVERT: A 897 ARG cc_start: 0.7176 (mmp-170) cc_final: 0.6300 (mtm110) REVERT: A 906 GLU cc_start: 0.8526 (OUTLIER) cc_final: 0.8122 (mm-30) REVERT: A 928 HIS cc_start: 0.4836 (m90) cc_final: 0.4431 (t-90) REVERT: A 935 GLU cc_start: 0.7473 (OUTLIER) cc_final: 0.6955 (mt-10) REVERT: D 337 ASP cc_start: 0.7414 (t0) cc_final: 0.7181 (m-30) REVERT: D 378 ILE cc_start: 0.7202 (OUTLIER) cc_final: 0.6980 (tt) REVERT: D 398 GLU cc_start: 0.6393 (pm20) cc_final: 0.6178 (pm20) REVERT: D 439 LEU cc_start: 0.7585 (OUTLIER) cc_final: 0.7339 (tp) REVERT: D 491 GLU cc_start: 0.8541 (mp0) cc_final: 0.8189 (mp0) REVERT: D 511 ILE cc_start: 0.7230 (mt) cc_final: 0.6909 (pp) REVERT: D 575 GLU cc_start: 0.7798 (mp0) cc_final: 0.7323 (mm-30) REVERT: D 615 GLU cc_start: 0.6247 (OUTLIER) cc_final: 0.5949 (pt0) REVERT: D 842 ARG cc_start: 0.8261 (mtp85) cc_final: 0.7947 (mtp180) REVERT: D 877 TRP cc_start: 0.7284 (m100) cc_final: 0.6754 (m-10) REVERT: D 897 ARG cc_start: 0.7174 (mmp-170) cc_final: 0.6293 (mtm110) REVERT: D 906 GLU cc_start: 0.8542 (OUTLIER) cc_final: 0.8142 (mm-30) REVERT: D 928 HIS cc_start: 0.4896 (m90) cc_final: 0.4364 (t70) REVERT: D 935 GLU cc_start: 0.7467 (OUTLIER) cc_final: 0.6946 (mt-10) REVERT: C 375 GLU cc_start: 0.7577 (mp0) cc_final: 0.7241 (mp0) REVERT: C 378 ILE cc_start: 0.7069 (OUTLIER) cc_final: 0.6761 (tt) REVERT: C 439 LEU cc_start: 0.7581 (OUTLIER) cc_final: 0.7334 (tp) REVERT: C 491 GLU cc_start: 0.8547 (mp0) cc_final: 0.8229 (mp0) REVERT: C 511 ILE cc_start: 0.7231 (mt) cc_final: 0.6912 (pp) REVERT: C 575 GLU cc_start: 0.7794 (mp0) cc_final: 0.7326 (mm-30) REVERT: C 615 GLU cc_start: 0.6265 (OUTLIER) cc_final: 0.5965 (pt0) REVERT: C 842 ARG cc_start: 0.8252 (mtp85) cc_final: 0.7940 (mtp180) REVERT: C 877 TRP cc_start: 0.7285 (m100) cc_final: 0.6760 (m-10) REVERT: C 897 ARG cc_start: 0.7177 (mmp-170) cc_final: 0.6288 (mtm110) REVERT: C 906 GLU cc_start: 0.8537 (OUTLIER) cc_final: 0.8135 (mm-30) REVERT: C 928 HIS cc_start: 0.4888 (m90) cc_final: 0.4363 (t70) REVERT: C 935 GLU cc_start: 0.7478 (OUTLIER) cc_final: 0.6959 (mt-10) REVERT: B 191 TYR cc_start: 0.8035 (t80) cc_final: 0.7792 (t80) REVERT: B 378 ILE cc_start: 0.7183 (OUTLIER) cc_final: 0.6937 (tt) REVERT: B 439 LEU cc_start: 0.7589 (OUTLIER) cc_final: 0.7344 (tp) REVERT: B 491 GLU cc_start: 0.8560 (mp0) cc_final: 0.8208 (mp0) REVERT: B 511 ILE cc_start: 0.7220 (mt) cc_final: 0.6901 (pp) REVERT: B 575 GLU cc_start: 0.7797 (mp0) cc_final: 0.7328 (mm-30) REVERT: B 615 GLU cc_start: 0.6265 (OUTLIER) cc_final: 0.5971 (pt0) REVERT: B 842 ARG cc_start: 0.8255 (mtp85) cc_final: 0.7942 (mtp180) REVERT: B 877 TRP cc_start: 0.7284 (m100) cc_final: 0.6761 (m-10) REVERT: B 897 ARG cc_start: 0.7174 (mmp-170) cc_final: 0.6293 (mtm110) REVERT: B 906 GLU cc_start: 0.8546 (OUTLIER) cc_final: 0.8146 (mm-30) REVERT: B 928 HIS cc_start: 0.4895 (m90) cc_final: 0.4365 (t70) REVERT: B 935 GLU cc_start: 0.7462 (OUTLIER) cc_final: 0.6941 (mt-10) outliers start: 147 outliers final: 69 residues processed: 408 average time/residue: 0.5927 time to fit residues: 284.6893 Evaluate side-chains 376 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 289 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 587 CYS Chi-restraints excluded: chain A residue 615 GLU Chi-restraints excluded: chain A residue 624 ARG Chi-restraints excluded: chain A residue 686 ILE Chi-restraints excluded: chain A residue 758 MET Chi-restraints excluded: chain A residue 899 ILE Chi-restraints excluded: chain A residue 906 GLU Chi-restraints excluded: chain A residue 929 CYS Chi-restraints excluded: chain A residue 935 GLU Chi-restraints excluded: chain A residue 941 VAL Chi-restraints excluded: chain A residue 992 GLN Chi-restraints excluded: chain A residue 1004 GLU Chi-restraints excluded: chain D residue 201 ILE Chi-restraints excluded: chain D residue 225 THR Chi-restraints excluded: chain D residue 378 ILE Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 393 VAL Chi-restraints excluded: chain D residue 402 GLU Chi-restraints excluded: chain D residue 418 THR Chi-restraints excluded: chain D residue 439 LEU Chi-restraints excluded: chain D residue 446 ILE Chi-restraints excluded: chain D residue 587 CYS Chi-restraints excluded: chain D residue 615 GLU Chi-restraints excluded: chain D residue 624 ARG Chi-restraints excluded: chain D residue 686 ILE Chi-restraints excluded: chain D residue 758 MET Chi-restraints excluded: chain D residue 899 ILE Chi-restraints excluded: chain D residue 906 GLU Chi-restraints excluded: chain D residue 929 CYS Chi-restraints excluded: chain D residue 935 GLU Chi-restraints excluded: chain D residue 941 VAL Chi-restraints excluded: chain D residue 992 GLN Chi-restraints excluded: chain D residue 1004 GLU Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 378 ILE Chi-restraints excluded: chain C residue 385 LEU Chi-restraints excluded: chain C residue 393 VAL Chi-restraints excluded: chain C residue 402 GLU Chi-restraints excluded: chain C residue 403 ILE Chi-restraints excluded: chain C residue 418 THR Chi-restraints excluded: chain C residue 439 LEU Chi-restraints excluded: chain C residue 446 ILE Chi-restraints excluded: chain C residue 587 CYS Chi-restraints excluded: chain C residue 615 GLU Chi-restraints excluded: chain C residue 624 ARG Chi-restraints excluded: chain C residue 686 ILE Chi-restraints excluded: chain C residue 758 MET Chi-restraints excluded: chain C residue 899 ILE Chi-restraints excluded: chain C residue 901 ARG Chi-restraints excluded: chain C residue 906 GLU Chi-restraints excluded: chain C residue 929 CYS Chi-restraints excluded: chain C residue 935 GLU Chi-restraints excluded: chain C residue 941 VAL Chi-restraints excluded: chain C residue 992 GLN Chi-restraints excluded: chain C residue 1004 GLU Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 378 ILE Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 402 GLU Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 446 ILE Chi-restraints excluded: chain B residue 587 CYS Chi-restraints excluded: chain B residue 615 GLU Chi-restraints excluded: chain B residue 624 ARG Chi-restraints excluded: chain B residue 686 ILE Chi-restraints excluded: chain B residue 758 MET Chi-restraints excluded: chain B residue 899 ILE Chi-restraints excluded: chain B residue 901 ARG Chi-restraints excluded: chain B residue 906 GLU Chi-restraints excluded: chain B residue 929 CYS Chi-restraints excluded: chain B residue 935 GLU Chi-restraints excluded: chain B residue 941 VAL Chi-restraints excluded: chain B residue 992 GLN Chi-restraints excluded: chain B residue 1004 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 336 optimal weight: 2.9990 chunk 53 optimal weight: 10.0000 chunk 145 optimal weight: 10.0000 chunk 36 optimal weight: 6.9990 chunk 202 optimal weight: 10.0000 chunk 113 optimal weight: 3.9990 chunk 54 optimal weight: 0.7980 chunk 185 optimal weight: 20.0000 chunk 10 optimal weight: 10.0000 chunk 321 optimal weight: 0.9990 chunk 120 optimal weight: 6.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 671 GLN D 671 GLN C 671 GLN B 136 HIS B 671 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.190671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.127847 restraints weight = 35190.373| |-----------------------------------------------------------------------------| r_work (start): 0.3601 rms_B_bonded: 2.27 r_work: 0.3474 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3341 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.2508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 28868 Z= 0.182 Angle : 0.577 9.210 39188 Z= 0.306 Chirality : 0.040 0.145 4456 Planarity : 0.004 0.048 4844 Dihedral : 4.570 24.442 3984 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 5.40 % Allowed : 20.89 % Favored : 73.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.88 (0.14), residues: 3404 helix: 2.20 (0.10), residues: 2404 sheet: -0.98 (0.40), residues: 176 loop : -1.17 (0.20), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 162 TYR 0.018 0.002 TYR C 787 PHE 0.021 0.002 PHE C 779 TRP 0.017 0.002 TRP C 994 HIS 0.006 0.001 HIS C 389 Details of bonding type rmsd/Z covalent geometry : bond 0.00439 / 0.18 (28864) covalent geometry : angle 0.57558 / 0.31 (39180) SS BOND : bond 0.00056 / 0.03 ( 4) SS BOND : angle 2.85199 / 2.05 ( 8) hydrogen bonds : bond 0.06434 / 4.32 ( 1812) hydrogen bonds : angle 3.96928 / 2.84 ( 5400) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6808 Ramachandran restraints generated. 3404 Oldfield, 0 Emsley, 3404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6808 Ramachandran restraints generated. 3404 Oldfield, 0 Emsley, 3404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 464 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 163 poor density : 301 time to evaluate : 0.949 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 LEU cc_start: 0.6789 (mp) cc_final: 0.6385 (tt) REVERT: A 119 ARG cc_start: 0.5627 (OUTLIER) cc_final: 0.4930 (ptp90) REVERT: A 162 ARG cc_start: 0.7677 (mtt180) cc_final: 0.7296 (mpt-90) REVERT: A 214 ILE cc_start: 0.8645 (OUTLIER) cc_final: 0.8398 (tp) REVERT: A 439 LEU cc_start: 0.7666 (OUTLIER) cc_final: 0.7317 (tp) REVERT: A 491 GLU cc_start: 0.8625 (mp0) cc_final: 0.8237 (mp0) REVERT: A 575 GLU cc_start: 0.8039 (mp0) cc_final: 0.7528 (mm-30) REVERT: A 615 GLU cc_start: 0.6300 (OUTLIER) cc_final: 0.6031 (pt0) REVERT: A 842 ARG cc_start: 0.8437 (mtp85) cc_final: 0.8126 (mtp180) REVERT: A 877 TRP cc_start: 0.7385 (m100) cc_final: 0.6763 (m-10) REVERT: A 897 ARG cc_start: 0.7342 (mmp-170) cc_final: 0.6443 (mtm110) REVERT: A 906 GLU cc_start: 0.8691 (OUTLIER) cc_final: 0.8333 (mm-30) REVERT: A 928 HIS cc_start: 0.4996 (m90) cc_final: 0.4515 (t-90) REVERT: A 935 GLU cc_start: 0.7545 (OUTLIER) cc_final: 0.7054 (mt-10) REVERT: D 162 ARG cc_start: 0.7749 (mtt180) cc_final: 0.7314 (mpt-90) REVERT: D 214 ILE cc_start: 0.8662 (OUTLIER) cc_final: 0.8416 (tp) REVERT: D 378 ILE cc_start: 0.7242 (OUTLIER) cc_final: 0.6819 (tt) REVERT: D 439 LEU cc_start: 0.7683 (OUTLIER) cc_final: 0.7398 (tp) REVERT: D 491 GLU cc_start: 0.8605 (mp0) cc_final: 0.8225 (mp0) REVERT: D 511 ILE cc_start: 0.7236 (mt) cc_final: 0.6918 (pp) REVERT: D 575 GLU cc_start: 0.8043 (mp0) cc_final: 0.7536 (mm-30) REVERT: D 615 GLU cc_start: 0.6303 (OUTLIER) cc_final: 0.6055 (pt0) REVERT: D 842 ARG cc_start: 0.8400 (mtp85) cc_final: 0.8099 (mtp180) REVERT: D 897 ARG cc_start: 0.7335 (mmp-170) cc_final: 0.6443 (mtm110) REVERT: D 906 GLU cc_start: 0.8670 (OUTLIER) cc_final: 0.8301 (mm-30) REVERT: D 928 HIS cc_start: 0.4987 (m90) cc_final: 0.4421 (t70) REVERT: D 935 GLU cc_start: 0.7525 (OUTLIER) cc_final: 0.7028 (mt-10) REVERT: D 945 GLU cc_start: 0.7209 (OUTLIER) cc_final: 0.6594 (pp20) REVERT: C 162 ARG cc_start: 0.7699 (mtt180) cc_final: 0.7311 (mpt-90) REVERT: C 214 ILE cc_start: 0.8652 (OUTLIER) cc_final: 0.8411 (tp) REVERT: C 375 GLU cc_start: 0.7626 (mp0) cc_final: 0.7286 (mp0) REVERT: C 378 ILE cc_start: 0.7120 (OUTLIER) cc_final: 0.6849 (tt) REVERT: C 439 LEU cc_start: 0.7639 (OUTLIER) cc_final: 0.7371 (tp) REVERT: C 491 GLU cc_start: 0.8634 (mp0) cc_final: 0.8292 (mp0) REVERT: C 511 ILE cc_start: 0.7246 (mt) cc_final: 0.6932 (pp) REVERT: C 575 GLU cc_start: 0.8044 (mp0) cc_final: 0.7529 (mm-30) REVERT: C 615 GLU cc_start: 0.6338 (OUTLIER) cc_final: 0.6085 (pt0) REVERT: C 842 ARG cc_start: 0.8426 (mtp85) cc_final: 0.8127 (mtp180) REVERT: C 877 TRP cc_start: 0.7440 (m100) cc_final: 0.6840 (m-10) REVERT: C 897 ARG cc_start: 0.7341 (mmp-170) cc_final: 0.6443 (mtm110) REVERT: C 906 GLU cc_start: 0.8702 (OUTLIER) cc_final: 0.8342 (mm-30) REVERT: C 928 HIS cc_start: 0.5048 (m90) cc_final: 0.4457 (t70) REVERT: C 935 GLU cc_start: 0.7542 (OUTLIER) cc_final: 0.7062 (mt-10) REVERT: C 945 GLU cc_start: 0.7196 (OUTLIER) cc_final: 0.6585 (pp20) REVERT: B 162 ARG cc_start: 0.7700 (mtt180) cc_final: 0.7312 (mpt-90) REVERT: B 214 ILE cc_start: 0.8671 (OUTLIER) cc_final: 0.8426 (tp) REVERT: B 378 ILE cc_start: 0.7218 (OUTLIER) cc_final: 0.6749 (tt) REVERT: B 439 LEU cc_start: 0.7694 (OUTLIER) cc_final: 0.7407 (tp) REVERT: B 491 GLU cc_start: 0.8613 (mp0) cc_final: 0.8230 (mp0) REVERT: B 511 ILE cc_start: 0.7232 (mt) cc_final: 0.6919 (pp) REVERT: B 575 GLU cc_start: 0.8051 (mp0) cc_final: 0.7540 (mm-30) REVERT: B 615 GLU cc_start: 0.6328 (OUTLIER) cc_final: 0.6075 (pt0) REVERT: B 842 ARG cc_start: 0.8396 (mtp85) cc_final: 0.8092 (mtp180) REVERT: B 897 ARG cc_start: 0.7358 (mmp-170) cc_final: 0.6459 (mtm110) REVERT: B 906 GLU cc_start: 0.8680 (OUTLIER) cc_final: 0.8317 (mm-30) REVERT: B 928 HIS cc_start: 0.5023 (m90) cc_final: 0.4431 (t70) REVERT: B 935 GLU cc_start: 0.7519 (OUTLIER) cc_final: 0.7024 (mt-10) REVERT: B 945 GLU cc_start: 0.7189 (OUTLIER) cc_final: 0.6562 (pp20) outliers start: 163 outliers final: 70 residues processed: 422 average time/residue: 0.6291 time to fit residues: 311.3412 Evaluate side-chains 389 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 292 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 ARG Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 587 CYS Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 615 GLU Chi-restraints excluded: chain A residue 624 ARG Chi-restraints excluded: chain A residue 651 TRP Chi-restraints excluded: chain A residue 686 ILE Chi-restraints excluded: chain A residue 758 MET Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain A residue 899 ILE Chi-restraints excluded: chain A residue 906 GLU Chi-restraints excluded: chain A residue 929 CYS Chi-restraints excluded: chain A residue 935 GLU Chi-restraints excluded: chain A residue 941 VAL Chi-restraints excluded: chain A residue 992 GLN Chi-restraints excluded: chain A residue 1004 GLU Chi-restraints excluded: chain D residue 201 ILE Chi-restraints excluded: chain D residue 214 ILE Chi-restraints excluded: chain D residue 225 THR Chi-restraints excluded: chain D residue 378 ILE Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 393 VAL Chi-restraints excluded: chain D residue 402 GLU Chi-restraints excluded: chain D residue 418 THR Chi-restraints excluded: chain D residue 439 LEU Chi-restraints excluded: chain D residue 587 CYS Chi-restraints excluded: chain D residue 615 GLU Chi-restraints excluded: chain D residue 624 ARG Chi-restraints excluded: chain D residue 651 TRP Chi-restraints excluded: chain D residue 686 ILE Chi-restraints excluded: chain D residue 758 MET Chi-restraints excluded: chain D residue 783 VAL Chi-restraints excluded: chain D residue 899 ILE Chi-restraints excluded: chain D residue 906 GLU Chi-restraints excluded: chain D residue 929 CYS Chi-restraints excluded: chain D residue 935 GLU Chi-restraints excluded: chain D residue 941 VAL Chi-restraints excluded: chain D residue 945 GLU Chi-restraints excluded: chain D residue 992 GLN Chi-restraints excluded: chain D residue 1004 GLU Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 214 ILE Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 378 ILE Chi-restraints excluded: chain C residue 385 LEU Chi-restraints excluded: chain C residue 393 VAL Chi-restraints excluded: chain C residue 402 GLU Chi-restraints excluded: chain C residue 418 THR Chi-restraints excluded: chain C residue 439 LEU Chi-restraints excluded: chain C residue 587 CYS Chi-restraints excluded: chain C residue 615 GLU Chi-restraints excluded: chain C residue 624 ARG Chi-restraints excluded: chain C residue 651 TRP Chi-restraints excluded: chain C residue 686 ILE Chi-restraints excluded: chain C residue 758 MET Chi-restraints excluded: chain C residue 783 VAL Chi-restraints excluded: chain C residue 899 ILE Chi-restraints excluded: chain C residue 906 GLU Chi-restraints excluded: chain C residue 929 CYS Chi-restraints excluded: chain C residue 935 GLU Chi-restraints excluded: chain C residue 941 VAL Chi-restraints excluded: chain C residue 945 GLU Chi-restraints excluded: chain C residue 992 GLN Chi-restraints excluded: chain C residue 1004 GLU Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 378 ILE Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 587 CYS Chi-restraints excluded: chain B residue 615 GLU Chi-restraints excluded: chain B residue 624 ARG Chi-restraints excluded: chain B residue 651 TRP Chi-restraints excluded: chain B residue 686 ILE Chi-restraints excluded: chain B residue 758 MET Chi-restraints excluded: chain B residue 783 VAL Chi-restraints excluded: chain B residue 801 MET Chi-restraints excluded: chain B residue 899 ILE Chi-restraints excluded: chain B residue 906 GLU Chi-restraints excluded: chain B residue 929 CYS Chi-restraints excluded: chain B residue 935 GLU Chi-restraints excluded: chain B residue 941 VAL Chi-restraints excluded: chain B residue 945 GLU Chi-restraints excluded: chain B residue 992 GLN Chi-restraints excluded: chain B residue 1004 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 43 optimal weight: 2.9990 chunk 225 optimal weight: 0.0770 chunk 272 optimal weight: 20.0000 chunk 131 optimal weight: 0.0770 chunk 84 optimal weight: 7.9990 chunk 175 optimal weight: 30.0000 chunk 176 optimal weight: 8.9990 chunk 126 optimal weight: 10.0000 chunk 171 optimal weight: 8.9990 chunk 254 optimal weight: 4.9990 chunk 342 optimal weight: 0.9990 overall best weight: 1.8302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 671 GLN D 671 GLN C 671 GLN B 671 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.193140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.131166 restraints weight = 35362.716| |-----------------------------------------------------------------------------| r_work (start): 0.3627 rms_B_bonded: 2.54 r_work: 0.3491 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3358 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.2589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 28868 Z= 0.134 Angle : 0.532 9.369 39188 Z= 0.280 Chirality : 0.038 0.141 4456 Planarity : 0.003 0.039 4844 Dihedral : 4.404 24.737 3984 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 3.88 % Allowed : 22.65 % Favored : 73.47 % 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: 2.05 (0.15), residues: 3404 helix: 2.33 (0.10), residues: 2408 sheet: -0.92 (0.40), residues: 176 loop : -1.12 (0.20), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 162 TYR 0.018 0.001 TYR C 787 PHE 0.014 0.001 PHE B 752 TRP 0.020 0.001 TRP C 994 HIS 0.006 0.001 HIS D 389 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.13 (28864) covalent geometry : angle 0.53054 / 0.28 (39180) SS BOND : bond 0.00080 / 0.04 ( 4) SS BOND : angle 2.91723 / 2.08 ( 8) hydrogen bonds : bond 0.05329 / 3.57 ( 1812) hydrogen bonds : angle 3.83625 / 2.74 ( 5400) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6808 Ramachandran restraints generated. 3404 Oldfield, 0 Emsley, 3404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6808 Ramachandran restraints generated. 3404 Oldfield, 0 Emsley, 3404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 305 time to evaluate : 1.042 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 186 TYR cc_start: 0.7724 (m-80) cc_final: 0.7332 (m-80) REVERT: A 398 GLU cc_start: 0.6625 (pm20) cc_final: 0.6281 (pm20) REVERT: A 439 LEU cc_start: 0.7601 (OUTLIER) cc_final: 0.7266 (tp) REVERT: A 491 GLU cc_start: 0.8656 (mp0) cc_final: 0.8302 (mp0) REVERT: A 575 GLU cc_start: 0.7978 (mp0) cc_final: 0.7394 (mm-30) REVERT: A 615 GLU cc_start: 0.6201 (OUTLIER) cc_final: 0.5968 (pt0) REVERT: A 842 ARG cc_start: 0.8402 (mtp85) cc_final: 0.8030 (mtp180) REVERT: A 877 TRP cc_start: 0.7387 (m100) cc_final: 0.6708 (m-10) REVERT: A 897 ARG cc_start: 0.7232 (mmp-170) cc_final: 0.6254 (mtm110) REVERT: A 906 GLU cc_start: 0.8697 (OUTLIER) cc_final: 0.8355 (mm-30) REVERT: A 928 HIS cc_start: 0.4921 (m90) cc_final: 0.4318 (t70) REVERT: D 171 ILE cc_start: 0.7429 (OUTLIER) cc_final: 0.7166 (mt) REVERT: D 186 TYR cc_start: 0.7739 (m-80) cc_final: 0.7482 (m-80) REVERT: D 491 GLU cc_start: 0.8645 (mp0) cc_final: 0.8294 (mp0) REVERT: D 511 ILE cc_start: 0.7185 (mt) cc_final: 0.6878 (pp) REVERT: D 575 GLU cc_start: 0.7974 (mp0) cc_final: 0.7394 (mm-30) REVERT: D 615 GLU cc_start: 0.6141 (OUTLIER) cc_final: 0.5927 (pt0) REVERT: D 842 ARG cc_start: 0.8361 (mtp85) cc_final: 0.7988 (mtp180) REVERT: D 877 TRP cc_start: 0.7440 (m100) cc_final: 0.6778 (m-10) REVERT: D 897 ARG cc_start: 0.7231 (mmp-170) cc_final: 0.6249 (mtm110) REVERT: D 906 GLU cc_start: 0.8684 (OUTLIER) cc_final: 0.8338 (mm-30) REVERT: D 928 HIS cc_start: 0.4887 (m90) cc_final: 0.4251 (t70) REVERT: C 171 ILE cc_start: 0.7443 (OUTLIER) cc_final: 0.7173 (mt) REVERT: C 186 TYR cc_start: 0.7723 (m-80) cc_final: 0.7511 (m-80) REVERT: C 338 VAL cc_start: 0.6974 (t) cc_final: 0.6770 (t) REVERT: C 375 GLU cc_start: 0.7625 (mp0) cc_final: 0.7273 (mp0) REVERT: C 439 LEU cc_start: 0.7585 (OUTLIER) cc_final: 0.7316 (tp) REVERT: C 491 GLU cc_start: 0.8680 (mp0) cc_final: 0.8340 (mp0) REVERT: C 511 ILE cc_start: 0.7186 (mt) cc_final: 0.6888 (pp) REVERT: C 575 GLU cc_start: 0.7981 (mp0) cc_final: 0.7390 (mm-30) REVERT: C 615 GLU cc_start: 0.6218 (OUTLIER) cc_final: 0.5993 (pt0) REVERT: C 842 ARG cc_start: 0.8396 (mtp85) cc_final: 0.8030 (mtp180) REVERT: C 877 TRP cc_start: 0.7430 (m100) cc_final: 0.6750 (m-10) REVERT: C 897 ARG cc_start: 0.7226 (mmp-170) cc_final: 0.6246 (mtm110) REVERT: C 906 GLU cc_start: 0.8711 (OUTLIER) cc_final: 0.8372 (mm-30) REVERT: C 928 HIS cc_start: 0.4888 (m90) cc_final: 0.4265 (t70) REVERT: B 171 ILE cc_start: 0.7413 (OUTLIER) cc_final: 0.7147 (mt) REVERT: B 338 VAL cc_start: 0.6970 (t) cc_final: 0.6749 (t) REVERT: B 491 GLU cc_start: 0.8656 (mp0) cc_final: 0.8300 (mp0) REVERT: B 511 ILE cc_start: 0.7176 (mt) cc_final: 0.6874 (pp) REVERT: B 575 GLU cc_start: 0.7981 (mp0) cc_final: 0.7400 (mm-30) REVERT: B 615 GLU cc_start: 0.6164 (OUTLIER) cc_final: 0.5950 (pt0) REVERT: B 842 ARG cc_start: 0.8364 (mtp85) cc_final: 0.7991 (mtp180) REVERT: B 877 TRP cc_start: 0.7447 (m100) cc_final: 0.6778 (m-10) REVERT: B 897 ARG cc_start: 0.7232 (mmp-170) cc_final: 0.6249 (mtm110) REVERT: B 906 GLU cc_start: 0.8682 (OUTLIER) cc_final: 0.8334 (mm-30) REVERT: B 928 HIS cc_start: 0.4891 (m90) cc_final: 0.4251 (t70) outliers start: 117 outliers final: 61 residues processed: 404 average time/residue: 0.5890 time to fit residues: 282.6710 Evaluate side-chains 358 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 284 time to evaluate : 1.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 587 CYS Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 615 GLU Chi-restraints excluded: chain A residue 624 ARG Chi-restraints excluded: chain A residue 686 ILE Chi-restraints excluded: chain A residue 758 MET Chi-restraints excluded: chain A residue 899 ILE Chi-restraints excluded: chain A residue 901 ARG Chi-restraints excluded: chain A residue 906 GLU Chi-restraints excluded: chain A residue 929 CYS Chi-restraints excluded: chain A residue 985 ILE Chi-restraints excluded: chain A residue 992 GLN Chi-restraints excluded: chain A residue 1004 GLU Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 201 ILE Chi-restraints excluded: chain D residue 225 THR Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 393 VAL Chi-restraints excluded: chain D residue 418 THR Chi-restraints excluded: chain D residue 587 CYS Chi-restraints excluded: chain D residue 615 GLU Chi-restraints excluded: chain D residue 624 ARG Chi-restraints excluded: chain D residue 686 ILE Chi-restraints excluded: chain D residue 758 MET Chi-restraints excluded: chain D residue 783 VAL Chi-restraints excluded: chain D residue 899 ILE Chi-restraints excluded: chain D residue 901 ARG Chi-restraints excluded: chain D residue 906 GLU Chi-restraints excluded: chain D residue 929 CYS Chi-restraints excluded: chain D residue 985 ILE Chi-restraints excluded: chain D residue 992 GLN Chi-restraints excluded: chain D residue 1004 GLU Chi-restraints excluded: chain C residue 171 ILE Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 393 VAL Chi-restraints excluded: chain C residue 403 ILE Chi-restraints excluded: chain C residue 418 THR Chi-restraints excluded: chain C residue 439 LEU Chi-restraints excluded: chain C residue 587 CYS Chi-restraints excluded: chain C residue 615 GLU Chi-restraints excluded: chain C residue 624 ARG Chi-restraints excluded: chain C residue 686 ILE Chi-restraints excluded: chain C residue 758 MET Chi-restraints excluded: chain C residue 783 VAL Chi-restraints excluded: chain C residue 899 ILE Chi-restraints excluded: chain C residue 906 GLU Chi-restraints excluded: chain C residue 929 CYS Chi-restraints excluded: chain C residue 985 ILE Chi-restraints excluded: chain C residue 992 GLN Chi-restraints excluded: chain C residue 1004 GLU Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain B residue 587 CYS Chi-restraints excluded: chain B residue 615 GLU Chi-restraints excluded: chain B residue 624 ARG Chi-restraints excluded: chain B residue 686 ILE Chi-restraints excluded: chain B residue 758 MET Chi-restraints excluded: chain B residue 783 VAL Chi-restraints excluded: chain B residue 899 ILE Chi-restraints excluded: chain B residue 906 GLU Chi-restraints excluded: chain B residue 929 CYS Chi-restraints excluded: chain B residue 992 GLN Chi-restraints excluded: chain B residue 1004 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 297 optimal weight: 7.9990 chunk 13 optimal weight: 8.9990 chunk 133 optimal weight: 2.9990 chunk 126 optimal weight: 8.9990 chunk 231 optimal weight: 1.9990 chunk 163 optimal weight: 1.9990 chunk 230 optimal weight: 1.9990 chunk 48 optimal weight: 4.9990 chunk 274 optimal weight: 20.0000 chunk 92 optimal weight: 6.9990 chunk 121 optimal weight: 3.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 671 GLN D 671 GLN C 671 GLN B 136 HIS B 671 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.191708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.129893 restraints weight = 35158.960| |-----------------------------------------------------------------------------| r_work (start): 0.3617 rms_B_bonded: 2.56 r_work: 0.3449 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.2680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 28868 Z= 0.161 Angle : 0.565 9.352 39188 Z= 0.299 Chirality : 0.040 0.166 4456 Planarity : 0.004 0.045 4844 Dihedral : 4.528 26.255 3984 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 4.05 % Allowed : 22.91 % Favored : 73.04 % 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: 1.93 (0.15), residues: 3404 helix: 2.23 (0.10), residues: 2400 sheet: -0.90 (0.40), residues: 176 loop : -1.14 (0.20), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 162 TYR 0.015 0.001 TYR B 186 PHE 0.025 0.002 PHE A 779 TRP 0.018 0.002 TRP C 994 HIS 0.006 0.001 HIS A 389 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.16 (28864) covalent geometry : angle 0.56379 / 0.30 (39180) SS BOND : bond 0.00061 / 0.03 ( 4) SS BOND : angle 2.92765 / 2.10 ( 8) hydrogen bonds : bond 0.05974 / 4.01 ( 1812) hydrogen bonds : angle 3.93208 / 2.82 ( 5400) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6808 Ramachandran restraints generated. 3404 Oldfield, 0 Emsley, 3404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6808 Ramachandran restraints generated. 3404 Oldfield, 0 Emsley, 3404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 300 time to evaluate : 1.054 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 439 LEU cc_start: 0.7662 (OUTLIER) cc_final: 0.7314 (tp) REVERT: A 491 GLU cc_start: 0.8587 (mp0) cc_final: 0.8203 (mp0) REVERT: A 575 GLU cc_start: 0.7762 (mp0) cc_final: 0.7375 (mm-30) REVERT: A 615 GLU cc_start: 0.6346 (OUTLIER) cc_final: 0.6051 (pt0) REVERT: A 842 ARG cc_start: 0.8287 (mtp85) cc_final: 0.7987 (mtp180) REVERT: A 877 TRP cc_start: 0.7267 (m100) cc_final: 0.6745 (m-10) REVERT: A 897 ARG cc_start: 0.7185 (mmp-170) cc_final: 0.6372 (mtm110) REVERT: A 906 GLU cc_start: 0.8499 (OUTLIER) cc_final: 0.8103 (mm-30) REVERT: A 928 HIS cc_start: 0.4802 (m90) cc_final: 0.4382 (t70) REVERT: A 935 GLU cc_start: 0.7576 (OUTLIER) cc_final: 0.7045 (mt-10) REVERT: D 439 LEU cc_start: 0.7677 (OUTLIER) cc_final: 0.7387 (tp) REVERT: D 491 GLU cc_start: 0.8595 (mp0) cc_final: 0.8216 (mp0) REVERT: D 511 ILE cc_start: 0.7272 (mt) cc_final: 0.6980 (pp) REVERT: D 575 GLU cc_start: 0.7746 (mp0) cc_final: 0.7377 (mm-30) REVERT: D 615 GLU cc_start: 0.6346 (OUTLIER) cc_final: 0.6070 (pt0) REVERT: D 842 ARG cc_start: 0.8266 (mtp85) cc_final: 0.7974 (mtp180) REVERT: D 897 ARG cc_start: 0.7192 (mmp-170) cc_final: 0.6373 (mtm110) REVERT: D 906 GLU cc_start: 0.8478 (OUTLIER) cc_final: 0.8075 (mm-30) REVERT: D 928 HIS cc_start: 0.4740 (m90) cc_final: 0.4344 (t70) REVERT: D 935 GLU cc_start: 0.7591 (OUTLIER) cc_final: 0.7063 (mt-10) REVERT: C 338 VAL cc_start: 0.7048 (t) cc_final: 0.6825 (t) REVERT: C 439 LEU cc_start: 0.7635 (OUTLIER) cc_final: 0.7341 (tp) REVERT: C 491 GLU cc_start: 0.8543 (mp0) cc_final: 0.8191 (mp0) REVERT: C 511 ILE cc_start: 0.7295 (mt) cc_final: 0.7010 (pp) REVERT: C 575 GLU cc_start: 0.7774 (mp0) cc_final: 0.7373 (mm-30) REVERT: C 615 GLU cc_start: 0.6398 (OUTLIER) cc_final: 0.6109 (pt0) REVERT: C 842 ARG cc_start: 0.8279 (mtp85) cc_final: 0.7985 (mtp180) REVERT: C 877 TRP cc_start: 0.7327 (m100) cc_final: 0.6819 (m-10) REVERT: C 897 ARG cc_start: 0.7184 (mmp-170) cc_final: 0.6369 (mtm110) REVERT: C 906 GLU cc_start: 0.8503 (OUTLIER) cc_final: 0.8111 (mm-30) REVERT: C 928 HIS cc_start: 0.4761 (m90) cc_final: 0.4354 (t70) REVERT: C 935 GLU cc_start: 0.7596 (OUTLIER) cc_final: 0.7075 (mt-10) REVERT: B 132 LEU cc_start: 0.5740 (OUTLIER) cc_final: 0.5455 (tp) REVERT: B 338 VAL cc_start: 0.7112 (t) cc_final: 0.6901 (t) REVERT: B 439 LEU cc_start: 0.7686 (OUTLIER) cc_final: 0.7392 (tp) REVERT: B 491 GLU cc_start: 0.8596 (mp0) cc_final: 0.8218 (mp0) REVERT: B 511 ILE cc_start: 0.7267 (mt) cc_final: 0.6974 (pp) REVERT: B 575 GLU cc_start: 0.7751 (mp0) cc_final: 0.7374 (mm-30) REVERT: B 615 GLU cc_start: 0.6345 (OUTLIER) cc_final: 0.6069 (pt0) REVERT: B 842 ARG cc_start: 0.8257 (mtp85) cc_final: 0.7964 (mtp180) REVERT: B 897 ARG cc_start: 0.7199 (mmp-170) cc_final: 0.6381 (mtm110) REVERT: B 906 GLU cc_start: 0.8487 (OUTLIER) cc_final: 0.8089 (mm-30) REVERT: B 928 HIS cc_start: 0.4749 (m90) cc_final: 0.4344 (t70) REVERT: B 935 GLU cc_start: 0.7571 (OUTLIER) cc_final: 0.7045 (mt-10) outliers start: 122 outliers final: 72 residues processed: 395 average time/residue: 0.5910 time to fit residues: 276.1984 Evaluate side-chains 377 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 288 time to evaluate : 1.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 587 CYS Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 615 GLU Chi-restraints excluded: chain A residue 624 ARG Chi-restraints excluded: chain A residue 651 TRP Chi-restraints excluded: chain A residue 686 ILE Chi-restraints excluded: chain A residue 758 MET Chi-restraints excluded: chain A residue 899 ILE Chi-restraints excluded: chain A residue 901 ARG Chi-restraints excluded: chain A residue 906 GLU Chi-restraints excluded: chain A residue 929 CYS Chi-restraints excluded: chain A residue 935 GLU Chi-restraints excluded: chain A residue 941 VAL Chi-restraints excluded: chain A residue 985 ILE Chi-restraints excluded: chain A residue 992 GLN Chi-restraints excluded: chain A residue 1004 GLU Chi-restraints excluded: chain D residue 201 ILE Chi-restraints excluded: chain D residue 225 THR Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 393 VAL Chi-restraints excluded: chain D residue 418 THR Chi-restraints excluded: chain D residue 439 LEU Chi-restraints excluded: chain D residue 587 CYS Chi-restraints excluded: chain D residue 615 GLU Chi-restraints excluded: chain D residue 624 ARG Chi-restraints excluded: chain D residue 651 TRP Chi-restraints excluded: chain D residue 686 ILE Chi-restraints excluded: chain D residue 758 MET Chi-restraints excluded: chain D residue 783 VAL Chi-restraints excluded: chain D residue 899 ILE Chi-restraints excluded: chain D residue 901 ARG Chi-restraints excluded: chain D residue 906 GLU Chi-restraints excluded: chain D residue 929 CYS Chi-restraints excluded: chain D residue 935 GLU Chi-restraints excluded: chain D residue 985 ILE Chi-restraints excluded: chain D residue 992 GLN Chi-restraints excluded: chain D residue 1004 GLU Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 385 LEU Chi-restraints excluded: chain C residue 393 VAL Chi-restraints excluded: chain C residue 403 ILE Chi-restraints excluded: chain C residue 418 THR Chi-restraints excluded: chain C residue 439 LEU Chi-restraints excluded: chain C residue 587 CYS Chi-restraints excluded: chain C residue 615 GLU Chi-restraints excluded: chain C residue 624 ARG Chi-restraints excluded: chain C residue 651 TRP Chi-restraints excluded: chain C residue 686 ILE Chi-restraints excluded: chain C residue 758 MET Chi-restraints excluded: chain C residue 783 VAL Chi-restraints excluded: chain C residue 899 ILE Chi-restraints excluded: chain C residue 906 GLU Chi-restraints excluded: chain C residue 929 CYS Chi-restraints excluded: chain C residue 935 GLU Chi-restraints excluded: chain C residue 941 VAL Chi-restraints excluded: chain C residue 985 ILE Chi-restraints excluded: chain C residue 992 GLN Chi-restraints excluded: chain C residue 1004 GLU Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 587 CYS Chi-restraints excluded: chain B residue 615 GLU Chi-restraints excluded: chain B residue 624 ARG Chi-restraints excluded: chain B residue 651 TRP Chi-restraints excluded: chain B residue 686 ILE Chi-restraints excluded: chain B residue 758 MET Chi-restraints excluded: chain B residue 783 VAL Chi-restraints excluded: chain B residue 899 ILE Chi-restraints excluded: chain B residue 906 GLU Chi-restraints excluded: chain B residue 929 CYS Chi-restraints excluded: chain B residue 935 GLU Chi-restraints excluded: chain B residue 941 VAL Chi-restraints excluded: chain B residue 985 ILE Chi-restraints excluded: chain B residue 992 GLN Chi-restraints excluded: chain B residue 1004 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 47 optimal weight: 3.9990 chunk 25 optimal weight: 0.0050 chunk 265 optimal weight: 7.9990 chunk 123 optimal weight: 6.9990 chunk 107 optimal weight: 0.9990 chunk 310 optimal weight: 0.7980 chunk 171 optimal weight: 10.0000 chunk 132 optimal weight: 0.9990 chunk 150 optimal weight: 4.9990 chunk 120 optimal weight: 0.9990 chunk 263 optimal weight: 6.9990 overall best weight: 0.7600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 671 GLN A 987 GLN D 510 GLN D 671 GLN D 987 GLN C 510 GLN C 671 GLN C 987 GLN B 510 GLN B 671 GLN B 987 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4392 r_free = 0.4392 target = 0.199566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.141808 restraints weight = 35323.590| |-----------------------------------------------------------------------------| r_work (start): 0.3761 rms_B_bonded: 2.51 r_work: 0.3629 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3502 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.2865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 28868 Z= 0.106 Angle : 0.513 9.746 39188 Z= 0.270 Chirality : 0.037 0.168 4456 Planarity : 0.003 0.036 4844 Dihedral : 4.224 27.570 3984 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.06 % Allowed : 25.10 % Favored : 72.84 % 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: 2.21 (0.15), residues: 3404 helix: 2.43 (0.10), residues: 2404 sheet: -0.57 (0.40), residues: 168 loop : -1.06 (0.20), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 162 TYR 0.019 0.001 TYR B 787 PHE 0.012 0.001 PHE A 165 TRP 0.025 0.001 TRP D 994 HIS 0.006 0.001 HIS D 389 Details of bonding type rmsd/Z covalent geometry : bond 0.00218 / 0.11 (28864) covalent geometry : angle 0.51085 / 0.27 (39180) SS BOND : bond 0.00078 / 0.04 ( 4) SS BOND : angle 3.21947 / 2.22 ( 8) hydrogen bonds : bond 0.04082 / 2.73 ( 1812) hydrogen bonds : angle 3.75229 / 2.69 ( 5400) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6808 Ramachandran restraints generated. 3404 Oldfield, 0 Emsley, 3404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6808 Ramachandran restraints generated. 3404 Oldfield, 0 Emsley, 3404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 305 time to evaluate : 1.032 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 575 GLU cc_start: 0.7838 (mp0) cc_final: 0.7347 (mm-30) REVERT: A 842 ARG cc_start: 0.8310 (mtp85) cc_final: 0.7937 (mtp180) REVERT: A 877 TRP cc_start: 0.7400 (m100) cc_final: 0.6732 (m-10) REVERT: A 897 ARG cc_start: 0.7087 (mmp-170) cc_final: 0.6087 (mtm110) REVERT: A 906 GLU cc_start: 0.8621 (OUTLIER) cc_final: 0.8313 (mm-30) REVERT: A 928 HIS cc_start: 0.4791 (m90) cc_final: 0.4247 (t70) REVERT: D 171 ILE cc_start: 0.7456 (OUTLIER) cc_final: 0.7178 (mt) REVERT: D 186 TYR cc_start: 0.7851 (m-80) cc_final: 0.7581 (m-80) REVERT: D 575 GLU cc_start: 0.7801 (mp0) cc_final: 0.7346 (mm-30) REVERT: D 842 ARG cc_start: 0.8320 (mtp85) cc_final: 0.7947 (mtp180) REVERT: D 877 TRP cc_start: 0.7386 (m100) cc_final: 0.6744 (m-10) REVERT: D 897 ARG cc_start: 0.7086 (mmp-170) cc_final: 0.6090 (mtm110) REVERT: D 906 GLU cc_start: 0.8661 (OUTLIER) cc_final: 0.8354 (mm-30) REVERT: D 928 HIS cc_start: 0.4739 (m90) cc_final: 0.4206 (t70) REVERT: C 171 ILE cc_start: 0.7406 (OUTLIER) cc_final: 0.7130 (mt) REVERT: C 186 TYR cc_start: 0.7838 (m-80) cc_final: 0.7619 (m-80) REVERT: C 337 ASP cc_start: 0.6168 (m-30) cc_final: 0.5663 (t0) REVERT: C 575 GLU cc_start: 0.7830 (mp0) cc_final: 0.7344 (mm-30) REVERT: C 842 ARG cc_start: 0.8297 (mtp85) cc_final: 0.7928 (mtp180) REVERT: C 877 TRP cc_start: 0.7431 (m100) cc_final: 0.6764 (m-10) REVERT: C 897 ARG cc_start: 0.7092 (mmp-170) cc_final: 0.6099 (mtm110) REVERT: C 906 GLU cc_start: 0.8619 (OUTLIER) cc_final: 0.8307 (mm-30) REVERT: C 928 HIS cc_start: 0.4715 (m90) cc_final: 0.4219 (t70) REVERT: B 171 ILE cc_start: 0.7455 (OUTLIER) cc_final: 0.7172 (mt) REVERT: B 338 VAL cc_start: 0.6832 (t) cc_final: 0.6538 (t) REVERT: B 439 LEU cc_start: 0.7663 (OUTLIER) cc_final: 0.7368 (tp) REVERT: B 575 GLU cc_start: 0.7803 (mp0) cc_final: 0.7343 (mm-30) REVERT: B 842 ARG cc_start: 0.8323 (mtp85) cc_final: 0.7951 (mtp180) REVERT: B 877 TRP cc_start: 0.7377 (m100) cc_final: 0.6743 (m-10) REVERT: B 897 ARG cc_start: 0.7112 (mmp-170) cc_final: 0.6118 (mtm110) REVERT: B 906 GLU cc_start: 0.8655 (OUTLIER) cc_final: 0.8347 (mm-30) REVERT: B 928 HIS cc_start: 0.4725 (m90) cc_final: 0.4223 (t70) outliers start: 62 outliers final: 31 residues processed: 354 average time/residue: 0.6073 time to fit residues: 254.0343 Evaluate side-chains 316 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 277 time to evaluate : 1.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 587 CYS Chi-restraints excluded: chain A residue 624 ARG Chi-restraints excluded: chain A residue 686 ILE Chi-restraints excluded: chain A residue 901 ARG Chi-restraints excluded: chain A residue 906 GLU Chi-restraints excluded: chain A residue 929 CYS Chi-restraints excluded: chain A residue 992 GLN Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 225 THR Chi-restraints excluded: chain D residue 587 CYS Chi-restraints excluded: chain D residue 624 ARG Chi-restraints excluded: chain D residue 686 ILE Chi-restraints excluded: chain D residue 901 ARG Chi-restraints excluded: chain D residue 906 GLU Chi-restraints excluded: chain D residue 929 CYS Chi-restraints excluded: chain D residue 992 GLN Chi-restraints excluded: chain C residue 171 ILE Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 385 LEU Chi-restraints excluded: chain C residue 403 ILE Chi-restraints excluded: chain C residue 587 CYS Chi-restraints excluded: chain C residue 624 ARG Chi-restraints excluded: chain C residue 686 ILE Chi-restraints excluded: chain C residue 906 GLU Chi-restraints excluded: chain C residue 929 CYS Chi-restraints excluded: chain C residue 992 GLN Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 587 CYS Chi-restraints excluded: chain B residue 624 ARG Chi-restraints excluded: chain B residue 686 ILE Chi-restraints excluded: chain B residue 906 GLU Chi-restraints excluded: chain B residue 929 CYS Chi-restraints excluded: chain B residue 992 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 26 optimal weight: 0.8980 chunk 163 optimal weight: 1.9990 chunk 131 optimal weight: 0.0070 chunk 94 optimal weight: 9.9990 chunk 42 optimal weight: 0.9990 chunk 63 optimal weight: 6.9990 chunk 202 optimal weight: 0.9990 chunk 320 optimal weight: 3.9990 chunk 339 optimal weight: 0.9990 chunk 329 optimal weight: 6.9990 chunk 273 optimal weight: 20.0000 overall best weight: 0.7804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 510 GLN A 987 GLN D 987 GLN C 306 GLN C 987 GLN B 306 GLN B 987 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4392 r_free = 0.4392 target = 0.199431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.140689 restraints weight = 35291.473| |-----------------------------------------------------------------------------| r_work (start): 0.3749 rms_B_bonded: 2.49 r_work: 0.3626 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3500 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.2951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 28868 Z= 0.108 Angle : 0.525 10.959 39188 Z= 0.275 Chirality : 0.037 0.173 4456 Planarity : 0.003 0.039 4844 Dihedral : 4.142 26.968 3984 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.59 % Allowed : 25.80 % Favored : 72.61 % 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: 2.23 (0.15), residues: 3404 helix: 2.41 (0.10), residues: 2420 sheet: -0.55 (0.40), residues: 168 loop : -1.01 (0.20), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 162 TYR 0.016 0.001 TYR A 186 PHE 0.022 0.001 PHE B 779 TRP 0.023 0.001 TRP C 994 HIS 0.006 0.001 HIS B 389 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.11 (28864) covalent geometry : angle 0.52294 / 0.27 (39180) SS BOND : bond 0.00067 / 0.03 ( 4) SS BOND : angle 2.96032 / 2.07 ( 8) hydrogen bonds : bond 0.04184 / 2.80 ( 1812) hydrogen bonds : angle 3.73369 / 2.68 ( 5400) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11114.03 seconds wall clock time: 189 minutes 43.67 seconds (11383.67 seconds total)