Starting phenix.real_space_refine on Fri Mar 6 16:19:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ud8_20734/03_2026/6ud8_20734_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ud8_20734/03_2026/6ud8_20734.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6ud8_20734/03_2026/6ud8_20734_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ud8_20734/03_2026/6ud8_20734_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6ud8_20734/03_2026/6ud8_20734.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ud8_20734/03_2026/6ud8_20734.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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: 7 Type Number sf(0) Gaussians P 4 5.49 5 S 120 5.16 5 C 10682 2.51 5 N 2524 2.21 5 O 2838 1.98 5 F 12 1.80 5 H 15482 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 72 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 31662 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 5675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 378, 5675 Classifications: {'peptide': 378} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 366} Chain breaks: 2 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 85 Unresolved non-hydrogen angles: 95 Unresolved non-hydrogen dihedrals: 76 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 2, 'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 31 Chain: "B" Number of atoms: 5742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 378, 5742 Classifications: {'peptide': 378} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 366} Chain breaks: 2 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 29 Chain: "E" Number of atoms: 2107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 2107 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 3, 'TRANS': 128} Chain breaks: 2 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 3, 'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "F" Number of atoms: 2147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 2147 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 2, 'TRANS': 131} Chain breaks: 2 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'HIS:plan': 1, 'ARG:plan': 3, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "C" Number of atoms: 5675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 378, 5675 Classifications: {'peptide': 378} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 366} Chain breaks: 2 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 85 Unresolved non-hydrogen angles: 95 Unresolved non-hydrogen dihedrals: 76 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 2, 'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 31 Chain: "D" Number of atoms: 5742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 378, 5742 Classifications: {'peptide': 378} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 366} Chain breaks: 2 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 29 Chain: "G" Number of atoms: 2107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 2107 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 3, 'TRANS': 128} Chain breaks: 2 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 3, 'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "H" Number of atoms: 2147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 2147 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 2, 'TRANS': 131} Chain breaks: 2 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'HIS:plan': 1, 'ARG:plan': 3, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "A" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 52 Unusual residues: {'OLC': 1, 'ZK1': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 52 Unusual residues: {'OLC': 1, 'ZK1': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 52 Unusual residues: {'OLC': 1, 'ZK1': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 52 Unusual residues: {'OLC': 1, 'ZK1': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.24, per 1000 atoms: 0.17 Number of scatterers: 31662 At special positions: 0 Unit cell: (118.326, 100.204, 146.042, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 120 16.00 P 4 15.00 F 12 9.00 O 2838 8.00 N 2524 7.00 C 10682 6.00 H 15482 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 718 " - pdb=" SG CYS A 773 " distance=2.03 Simple disulfide: pdb=" SG CYS B 718 " - pdb=" SG CYS B 773 " distance=2.03 Simple disulfide: pdb=" SG CYS C 718 " - pdb=" SG CYS C 773 " distance=2.03 Simple disulfide: pdb=" SG CYS D 718 " - pdb=" SG CYS D 773 " 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: 3.00 Conformation dependent library (CDL) restraints added in 967.5 milliseconds 3992 Ramachandran restraints generated. 1996 Oldfield, 0 Emsley, 1996 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3812 Finding SS restraints... Secondary structure from input PDB file: 82 helices and 18 sheets defined 62.5% alpha, 5.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.72 Creating SS restraints... Processing helix chain 'A' and resid 417 through 419 No H-bonds generated for 'chain 'A' and resid 417 through 419' Processing helix chain 'A' and resid 423 through 437 Processing helix chain 'A' and resid 461 through 469 Processing helix chain 'A' and resid 482 through 487 Processing helix chain 'A' and resid 515 through 519 Processing helix chain 'A' and resid 522 through 547 removed outlier: 3.959A pdb=" N CYS A 528 " --> pdb=" O GLU A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 629 Processing helix chain 'A' and resid 636 through 641 Processing helix chain 'A' and resid 653 through 660 Processing helix chain 'A' and resid 664 through 676 Processing helix chain 'A' and resid 685 through 696 removed outlier: 3.900A pdb=" N GLY A 689 " --> pdb=" O THR A 685 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N VAL A 693 " --> pdb=" O GLY A 689 " (cutoff:3.500A) Processing helix chain 'A' and resid 706 through 714 Processing helix chain 'A' and resid 742 through 756 removed outlier: 4.505A pdb=" N LEU A 748 " --> pdb=" O ASN A 744 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ALA A 749 " --> pdb=" O ALA A 745 " (cutoff:3.500A) Processing helix chain 'A' and resid 757 through 768 Processing helix chain 'A' and resid 788 through 791 Processing helix chain 'A' and resid 792 through 823 removed outlier: 3.720A pdb=" N PHE A 796 " --> pdb=" O VAL A 792 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA A 820 " --> pdb=" O TYR A 816 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 419 No H-bonds generated for 'chain 'B' and resid 417 through 419' Processing helix chain 'B' and resid 423 through 437 removed outlier: 3.706A pdb=" N ASP B 427 " --> pdb=" O GLY B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 463 through 469 Processing helix chain 'B' and resid 482 through 489 removed outlier: 3.697A pdb=" N VAL B 488 " --> pdb=" O VAL B 484 " (cutoff:3.500A) Processing helix chain 'B' and resid 522 through 542 Processing helix chain 'B' and resid 597 through 627 removed outlier: 3.616A pdb=" N VAL B 626 " --> pdb=" O ALA B 622 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLU B 627 " --> pdb=" O PHE B 623 " (cutoff:3.500A) Processing helix chain 'B' and resid 635 through 642 removed outlier: 3.978A pdb=" N LEU B 639 " --> pdb=" O SER B 635 " (cutoff:3.500A) Processing helix chain 'B' and resid 653 through 661 Processing helix chain 'B' and resid 666 through 676 Processing helix chain 'B' and resid 685 through 696 removed outlier: 3.853A pdb=" N GLY B 689 " --> pdb=" O THR B 685 " (cutoff:3.500A) Processing helix chain 'B' and resid 706 through 715 removed outlier: 3.562A pdb=" N GLN B 714 " --> pdb=" O GLU B 710 " (cutoff:3.500A) Processing helix chain 'B' and resid 742 through 756 removed outlier: 3.582A pdb=" N LEU B 751 " --> pdb=" O ASN B 747 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 768 Processing helix chain 'B' and resid 788 through 791 Processing helix chain 'B' and resid 792 through 824 removed outlier: 3.654A pdb=" N PHE B 796 " --> pdb=" O VAL B 792 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ARG B 819 " --> pdb=" O CYS B 815 " (cutoff:3.500A) Processing helix chain 'E' and resid 5 through 35 removed outlier: 3.927A pdb=" N CYS E 9 " --> pdb=" O PHE E 5 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALA E 19 " --> pdb=" O VAL E 15 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N PHE E 22 " --> pdb=" O ALA E 18 " (cutoff:3.500A) Processing helix chain 'E' and resid 51 through 67 removed outlier: 4.192A pdb=" N ILE E 60 " --> pdb=" O ASN E 56 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LEU E 63 " --> pdb=" O ARG E 59 " (cutoff:3.500A) Processing helix chain 'E' and resid 68 through 85 removed outlier: 3.748A pdb=" N TYR E 72 " --> pdb=" O VAL E 68 " (cutoff:3.500A) Processing helix chain 'E' and resid 94 through 107 Processing helix chain 'E' and resid 127 through 158 removed outlier: 3.544A pdb=" N PHE E 147 " --> pdb=" O LEU E 143 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL E 158 " --> pdb=" O ILE E 154 " (cutoff:3.500A) Processing helix chain 'F' and resid 5 through 38 removed outlier: 3.785A pdb=" N CYS F 9 " --> pdb=" O PHE F 5 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ALA F 19 " --> pdb=" O VAL F 15 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 67 Processing helix chain 'F' and resid 68 through 85 removed outlier: 3.672A pdb=" N TYR F 72 " --> pdb=" O VAL F 68 " (cutoff:3.500A) Processing helix chain 'F' and resid 90 through 106 Proline residue: F 96 - end of helix removed outlier: 3.809A pdb=" N TYR F 105 " --> pdb=" O HIS F 101 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N PHE F 106 " --> pdb=" O PHE F 102 " (cutoff:3.500A) Processing helix chain 'F' and resid 127 through 158 removed outlier: 4.317A pdb=" N LYS F 133 " --> pdb=" O SER F 129 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N VAL F 158 " --> pdb=" O ILE F 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 419 No H-bonds generated for 'chain 'C' and resid 417 through 419' Processing helix chain 'C' and resid 423 through 437 Processing helix chain 'C' and resid 461 through 469 Processing helix chain 'C' and resid 482 through 487 Processing helix chain 'C' and resid 515 through 519 Processing helix chain 'C' and resid 522 through 547 removed outlier: 3.958A pdb=" N CYS C 528 " --> pdb=" O GLU C 524 " (cutoff:3.500A) Processing helix chain 'C' and resid 596 through 629 Processing helix chain 'C' and resid 636 through 641 Processing helix chain 'C' and resid 653 through 660 Processing helix chain 'C' and resid 664 through 676 Processing helix chain 'C' and resid 685 through 696 removed outlier: 3.900A pdb=" N GLY C 689 " --> pdb=" O THR C 685 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VAL C 693 " --> pdb=" O GLY C 689 " (cutoff:3.500A) Processing helix chain 'C' and resid 706 through 714 Processing helix chain 'C' and resid 742 through 756 removed outlier: 4.505A pdb=" N LEU C 748 " --> pdb=" O ASN C 744 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N ALA C 749 " --> pdb=" O ALA C 745 " (cutoff:3.500A) Processing helix chain 'C' and resid 757 through 768 Processing helix chain 'C' and resid 788 through 791 Processing helix chain 'C' and resid 792 through 823 removed outlier: 3.718A pdb=" N PHE C 796 " --> pdb=" O VAL C 792 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA C 820 " --> pdb=" O TYR C 816 " (cutoff:3.500A) Processing helix chain 'D' and resid 417 through 419 No H-bonds generated for 'chain 'D' and resid 417 through 419' Processing helix chain 'D' and resid 423 through 437 removed outlier: 3.706A pdb=" N ASP D 427 " --> pdb=" O GLY D 423 " (cutoff:3.500A) Processing helix chain 'D' and resid 463 through 469 Processing helix chain 'D' and resid 482 through 489 removed outlier: 3.697A pdb=" N VAL D 488 " --> pdb=" O VAL D 484 " (cutoff:3.500A) Processing helix chain 'D' and resid 522 through 542 Processing helix chain 'D' and resid 597 through 627 removed outlier: 3.615A pdb=" N VAL D 626 " --> pdb=" O ALA D 622 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLU D 627 " --> pdb=" O PHE D 623 " (cutoff:3.500A) Processing helix chain 'D' and resid 635 through 642 removed outlier: 3.978A pdb=" N LEU D 639 " --> pdb=" O SER D 635 " (cutoff:3.500A) Processing helix chain 'D' and resid 653 through 661 Processing helix chain 'D' and resid 666 through 676 Processing helix chain 'D' and resid 685 through 696 removed outlier: 3.853A pdb=" N GLY D 689 " --> pdb=" O THR D 685 " (cutoff:3.500A) Processing helix chain 'D' and resid 706 through 715 removed outlier: 3.562A pdb=" N GLN D 714 " --> pdb=" O GLU D 710 " (cutoff:3.500A) Processing helix chain 'D' and resid 742 through 756 removed outlier: 3.581A pdb=" N LEU D 751 " --> pdb=" O ASN D 747 " (cutoff:3.500A) Processing helix chain 'D' and resid 758 through 768 Processing helix chain 'D' and resid 788 through 791 Processing helix chain 'D' and resid 792 through 824 removed outlier: 3.653A pdb=" N PHE D 796 " --> pdb=" O VAL D 792 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ARG D 819 " --> pdb=" O CYS D 815 " (cutoff:3.500A) Processing helix chain 'G' and resid 5 through 35 removed outlier: 3.927A pdb=" N CYS G 9 " --> pdb=" O PHE G 5 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALA G 19 " --> pdb=" O VAL G 15 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N PHE G 22 " --> pdb=" O ALA G 18 " (cutoff:3.500A) Processing helix chain 'G' and resid 51 through 67 removed outlier: 4.191A pdb=" N ILE G 60 " --> pdb=" O ASN G 56 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LEU G 63 " --> pdb=" O ARG G 59 " (cutoff:3.500A) Processing helix chain 'G' and resid 68 through 85 removed outlier: 3.748A pdb=" N TYR G 72 " --> pdb=" O VAL G 68 " (cutoff:3.500A) Processing helix chain 'G' and resid 94 through 107 Processing helix chain 'G' and resid 127 through 158 removed outlier: 3.545A pdb=" N PHE G 147 " --> pdb=" O LEU G 143 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N VAL G 158 " --> pdb=" O ILE G 154 " (cutoff:3.500A) Processing helix chain 'H' and resid 5 through 38 removed outlier: 3.785A pdb=" N CYS H 9 " --> pdb=" O PHE H 5 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ALA H 19 " --> pdb=" O VAL H 15 " (cutoff:3.500A) Processing helix chain 'H' and resid 49 through 67 Processing helix chain 'H' and resid 68 through 85 removed outlier: 3.672A pdb=" N TYR H 72 " --> pdb=" O VAL H 68 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 106 Proline residue: H 96 - end of helix removed outlier: 3.809A pdb=" N TYR H 105 " --> pdb=" O HIS H 101 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N PHE H 106 " --> pdb=" O PHE H 102 " (cutoff:3.500A) Processing helix chain 'H' and resid 127 through 158 removed outlier: 4.318A pdb=" N LYS H 133 " --> pdb=" O SER H 129 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N VAL H 158 " --> pdb=" O ILE H 154 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 440 through 444 removed outlier: 6.314A pdb=" N VAL A 395 " --> pdb=" O LYS A 441 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N THR A 443 " --> pdb=" O VAL A 395 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N VAL A 397 " --> pdb=" O THR A 443 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 407 through 408 Processing sheet with id=AA3, first strand: chain 'A' and resid 496 through 498 removed outlier: 3.670A pdb=" N MET A 496 " --> pdb=" O TYR A 732 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 646 through 648 removed outlier: 9.246A pdb=" N TYR A 700 " --> pdb=" O LYS A 505 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N LYS A 505 " --> pdb=" O TYR A 700 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE A 504 " --> pdb=" O MET A 721 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 396 through 397 Processing sheet with id=AA6, first strand: chain 'B' and resid 407 through 408 Processing sheet with id=AA7, first strand: chain 'B' and resid 451 through 452 Processing sheet with id=AA8, first strand: chain 'B' and resid 490 through 498 removed outlier: 4.320A pdb=" N ILE B 734 " --> pdb=" O SER B 492 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N TYR B 732 " --> pdb=" O PRO B 494 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N MET B 496 " --> pdb=" O LYS B 730 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N LYS B 730 " --> pdb=" O MET B 496 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 702 through 705 removed outlier: 4.423A pdb=" N ILE B 502 " --> pdb=" O VAL B 723 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N VAL B 723 " --> pdb=" O ILE B 502 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 440 through 444 removed outlier: 6.315A pdb=" N VAL C 395 " --> pdb=" O LYS C 441 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N THR C 443 " --> pdb=" O VAL C 395 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N VAL C 397 " --> pdb=" O THR C 443 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 407 through 408 Processing sheet with id=AB3, first strand: chain 'C' and resid 496 through 498 removed outlier: 3.670A pdb=" N MET C 496 " --> pdb=" O TYR C 732 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 646 through 648 removed outlier: 9.246A pdb=" N TYR C 700 " --> pdb=" O LYS C 505 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N LYS C 505 " --> pdb=" O TYR C 700 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE C 504 " --> pdb=" O MET C 721 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 396 through 397 Processing sheet with id=AB6, first strand: chain 'D' and resid 407 through 408 Processing sheet with id=AB7, first strand: chain 'D' and resid 451 through 452 Processing sheet with id=AB8, first strand: chain 'D' and resid 490 through 498 removed outlier: 4.319A pdb=" N ILE D 734 " --> pdb=" O SER D 492 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N TYR D 732 " --> pdb=" O PRO D 494 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N MET D 496 " --> pdb=" O LYS D 730 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N LYS D 730 " --> pdb=" O MET D 496 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 702 through 705 removed outlier: 4.423A pdb=" N ILE D 502 " --> pdb=" O VAL D 723 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N VAL D 723 " --> pdb=" O ILE D 502 " (cutoff:3.500A) 948 hydrogen bonds defined for protein. 2772 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: 7.48 Time building geometry restraints manager: 4.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 15430 1.04 - 1.25: 2172 1.25 - 1.45: 5169 1.45 - 1.65: 9107 1.65 - 1.86: 184 Bond restraints: 32062 Sorted by residual: bond pdb=" CAT ZK1 A 902 " pdb=" OAA ZK1 A 902 " ideal model delta sigma weight residual 1.214 1.397 -0.183 2.00e-02 2.50e+03 8.39e+01 bond pdb=" CAU ZK1 C 902 " pdb=" OAB ZK1 C 902 " ideal model delta sigma weight residual 1.215 1.397 -0.182 2.00e-02 2.50e+03 8.33e+01 bond pdb=" CAT ZK1 C 902 " pdb=" OAA ZK1 C 902 " ideal model delta sigma weight residual 1.214 1.396 -0.182 2.00e-02 2.50e+03 8.33e+01 bond pdb=" CAU ZK1 B 902 " pdb=" OAB ZK1 B 902 " ideal model delta sigma weight residual 1.215 1.397 -0.182 2.00e-02 2.50e+03 8.30e+01 bond pdb=" CAU ZK1 A 902 " pdb=" OAB ZK1 A 902 " ideal model delta sigma weight residual 1.215 1.397 -0.182 2.00e-02 2.50e+03 8.29e+01 ... (remaining 32057 not shown) Histogram of bond angle deviations from ideal: 0.00 - 11.29: 57562 11.29 - 22.57: 0 22.57 - 33.86: 6 33.86 - 45.15: 0 45.15 - 56.43: 4 Bond angle restraints: 57572 Sorted by residual: angle pdb=" C VAL A 445 " pdb=" N GLY A 446 " pdb=" H GLY A 446 " ideal model delta sigma weight residual 125.18 68.75 56.43 3.00e+00 1.11e-01 3.54e+02 angle pdb=" C VAL C 445 " pdb=" N GLY C 446 " pdb=" H GLY C 446 " ideal model delta sigma weight residual 125.18 68.75 56.43 3.00e+00 1.11e-01 3.54e+02 angle pdb=" CA GLY C 446 " pdb=" N GLY C 446 " pdb=" H GLY C 446 " ideal model delta sigma weight residual 114.88 58.60 56.28 3.00e+00 1.11e-01 3.52e+02 angle pdb=" CA GLY A 446 " pdb=" N GLY A 446 " pdb=" H GLY A 446 " ideal model delta sigma weight residual 114.88 58.61 56.27 3.00e+00 1.11e-01 3.52e+02 angle pdb=" CB LEU G 16 " pdb=" CG LEU G 16 " pdb=" HG LEU G 16 " ideal model delta sigma weight residual 109.00 84.70 24.30 3.00e+00 1.11e-01 6.56e+01 ... (remaining 57567 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.89: 15088 35.89 - 71.78: 374 71.78 - 107.68: 5 107.68 - 143.57: 9 143.57 - 179.46: 6 Dihedral angle restraints: 15482 sinusoidal: 8114 harmonic: 7368 Sorted by residual: dihedral pdb=" O20 OLC D 901 " pdb=" C21 OLC D 901 " pdb=" C22 OLC D 901 " pdb=" O23 OLC D 901 " ideal model delta sinusoidal sigma weight residual 302.77 123.31 179.46 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" O20 OLC B 901 " pdb=" C21 OLC B 901 " pdb=" C22 OLC B 901 " pdb=" O23 OLC B 901 " ideal model delta sinusoidal sigma weight residual 302.77 123.32 179.45 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C24 OLC B 901 " pdb=" C21 OLC B 901 " pdb=" C22 OLC B 901 " pdb=" O20 OLC B 901 " ideal model delta sinusoidal sigma weight residual -177.22 -3.71 -173.51 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 15479 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.343: 2538 0.343 - 0.687: 2 0.687 - 1.030: 0 1.030 - 1.373: 0 1.373 - 1.716: 4 Chirality restraints: 2544 Sorted by residual: chirality pdb=" CG LEU E 16 " pdb=" CB LEU E 16 " pdb=" CD1 LEU E 16 " pdb=" CD2 LEU E 16 " both_signs ideal model delta sigma weight residual False -2.59 -0.87 -1.72 2.00e-01 2.50e+01 7.36e+01 chirality pdb=" CG LEU G 16 " pdb=" CB LEU G 16 " pdb=" CD1 LEU G 16 " pdb=" CD2 LEU G 16 " both_signs ideal model delta sigma weight residual False -2.59 -0.88 -1.71 2.00e-01 2.50e+01 7.35e+01 chirality pdb=" C22 OLC C 901 " pdb=" C21 OLC C 901 " pdb=" C24 OLC C 901 " pdb=" O23 OLC C 901 " both_signs ideal model delta sigma weight residual False -2.31 -0.80 -1.51 2.00e-01 2.50e+01 5.72e+01 ... (remaining 2541 not shown) Planarity restraints: 4654 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C10 OLC D 901 " -0.191 2.00e-02 2.50e+03 1.89e-01 3.59e+02 pdb=" C11 OLC D 901 " 0.190 2.00e-02 2.50e+03 pdb=" C8 OLC D 901 " 0.189 2.00e-02 2.50e+03 pdb=" C9 OLC D 901 " -0.187 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 OLC B 901 " 0.191 2.00e-02 2.50e+03 1.89e-01 3.58e+02 pdb=" C11 OLC B 901 " -0.190 2.00e-02 2.50e+03 pdb=" C8 OLC B 901 " -0.189 2.00e-02 2.50e+03 pdb=" C9 OLC B 901 " 0.187 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 OLC A 901 " 0.155 2.00e-02 2.50e+03 1.55e-01 2.39e+02 pdb=" C11 OLC A 901 " -0.155 2.00e-02 2.50e+03 pdb=" C8 OLC A 901 " -0.154 2.00e-02 2.50e+03 pdb=" C9 OLC A 901 " 0.154 2.00e-02 2.50e+03 ... (remaining 4651 not shown) Histogram of nonbonded interaction distances: 1.54 - 2.15: 1033 2.15 - 2.76: 59988 2.76 - 3.37: 88904 3.37 - 3.99: 109253 3.99 - 4.60: 174337 Nonbonded interactions: 433515 Sorted by model distance: nonbonded pdb=" H GLY A 446 " pdb=" HA2 GLY A 446 " model vdw 1.536 1.816 nonbonded pdb=" H GLY C 446 " pdb=" HA2 GLY C 446 " model vdw 1.536 1.816 nonbonded pdb=" H ILE A 500 " pdb=" OD1 ASP A 728 " model vdw 1.557 2.450 nonbonded pdb=" H ILE C 500 " pdb=" OD1 ASP C 728 " model vdw 1.557 2.450 nonbonded pdb="HH12 ARG A 485 " pdb=" OAA ZK1 A 902 " model vdw 1.600 2.450 ... (remaining 433510 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'G' } ncs_group { reference = chain 'F' selection = chain 'H' } 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: 3.060 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: 0.180 Extract box with map and model: 0.480 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 29.630 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 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 : 0.008 0.183 16584 Z= 0.387 Angle : 0.644 10.432 22502 Z= 0.301 Chirality : 0.075 1.716 2544 Planarity : 0.007 0.189 2698 Dihedral : 14.526 179.461 6034 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % 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: -3.31 (0.16), residues: 1996 helix: -1.15 (0.13), residues: 1216 sheet: -3.04 (0.37), residues: 154 loop : -3.95 (0.19), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 628 TYR 0.015 0.001 TYR H 155 PHE 0.012 0.001 PHE A 546 TRP 0.010 0.001 TRP A 606 HIS 0.004 0.001 HIS H 75 Details of bonding type rmsd covalent geometry : bond 0.00793 (16580) covalent geometry : angle 0.64449 (22494) SS BOND : bond 0.00260 ( 4) SS BOND : angle 0.52001 ( 8) hydrogen bonds : bond 0.10787 ( 948) hydrogen bonds : angle 5.35005 ( 2772) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3992 Ramachandran restraints generated. 1996 Oldfield, 0 Emsley, 1996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3992 Ramachandran restraints generated. 1996 Oldfield, 0 Emsley, 1996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 409 is missing expected H atoms. Skipping. Residue LYS 410 is missing expected H atoms. Skipping. Residue MET 414 is missing expected H atoms. Skipping. Residue LYS 439 is missing expected H atoms. Skipping. Residue LYS 441 is missing expected H atoms. Skipping. Residue LYS 449 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue LYS 506 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue LEU 540 is missing expected H atoms. Skipping. Residue LYS 697 is missing expected H atoms. Skipping. Residue LYS 699 is missing expected H atoms. Skipping. Residue SER 729 is missing expected H atoms. Skipping. Residue LYS 823 is missing expected H atoms. Skipping. Residue LYS 409 is missing expected H atoms. Skipping. Residue LYS 410 is missing expected H atoms. Skipping. Residue MET 414 is missing expected H atoms. Skipping. Residue LYS 439 is missing expected H atoms. Skipping. Residue LYS 441 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue THR 784 is missing expected H atoms. Skipping. Residue SER 785 is missing expected H atoms. Skipping. Residue SER 788 is missing expected H atoms. Skipping. Residue LEU 54 is missing expected H atoms. Skipping. Residue ILE 57 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue VAL 48 is missing expected H atoms. Skipping. Residue LEU 54 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue THR 127 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Residue LYS 409 is missing expected H atoms. Skipping. Residue LYS 410 is missing expected H atoms. Skipping. Residue MET 414 is missing expected H atoms. Skipping. Residue LYS 439 is missing expected H atoms. Skipping. Residue LYS 441 is missing expected H atoms. Skipping. Residue LYS 449 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue LYS 506 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue LEU 540 is missing expected H atoms. Skipping. Residue LYS 697 is missing expected H atoms. Skipping. Residue LYS 699 is missing expected H atoms. Skipping. Residue SER 729 is missing expected H atoms. Skipping. Residue LYS 823 is missing expected H atoms. Skipping. Residue LYS 409 is missing expected H atoms. Skipping. Residue LYS 410 is missing expected H atoms. Skipping. Residue MET 414 is missing expected H atoms. Skipping. Residue LYS 439 is missing expected H atoms. Skipping. Residue LYS 441 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue THR 784 is missing expected H atoms. Skipping. Residue SER 785 is missing expected H atoms. Skipping. Residue SER 788 is missing expected H atoms. Skipping. Residue LEU 54 is missing expected H atoms. Skipping. Residue ILE 57 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue VAL 48 is missing expected H atoms. Skipping. Residue LEU 54 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue THR 127 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Evaluate side-chains 351 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 351 time to evaluate : 0.818 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: symmetry clash 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: B 713 GLU cc_start: 0.7962 (tt0) cc_final: 0.7648 (tm-30) REVERT: E 133 LYS cc_start: 0.6921 (mttm) cc_final: 0.6201 (ttpp) REVERT: F 81 MET cc_start: 0.7281 (ttm) cc_final: 0.6880 (ttm) REVERT: F 134 GLU cc_start: 0.8380 (tm-30) cc_final: 0.7727 (tt0) REVERT: C 633 ILE cc_start: 0.7233 (pt) cc_final: 0.6884 (pt) REVERT: D 713 GLU cc_start: 0.8017 (tt0) cc_final: 0.7654 (tm-30) REVERT: D 760 ASP cc_start: 0.7329 (p0) cc_final: 0.6933 (p0) REVERT: D 761 LYS cc_start: 0.8820 (tttt) cc_final: 0.8601 (tttt) REVERT: G 133 LYS cc_start: 0.7384 (mttm) cc_final: 0.7040 (tttm) REVERT: H 81 MET cc_start: 0.7574 (ttm) cc_final: 0.7134 (ttm) REVERT: H 138 LYS cc_start: 0.8266 (ttmm) cc_final: 0.8026 (tttt) outliers start: 0 outliers final: 0 residues processed: 351 average time/residue: 0.2953 time to fit residues: 152.8838 Evaluate side-chains 225 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 225 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 1.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 756 GLN A 764 ASN A 791 ASN B 791 ASN C 756 GLN C 764 ASN C 791 ASN D 791 ASN H 27 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.110761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.088439 restraints weight = 114883.843| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 3.19 r_work: 0.3307 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.2592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 16584 Z= 0.216 Angle : 0.597 10.739 22502 Z= 0.317 Chirality : 0.062 1.721 2544 Planarity : 0.005 0.073 2698 Dihedral : 12.536 179.606 2636 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 0.80 % Allowed : 9.80 % Favored : 89.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % 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: -1.54 (0.18), residues: 1996 helix: 0.13 (0.14), residues: 1232 sheet: -2.71 (0.41), residues: 144 loop : -2.90 (0.23), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 59 TYR 0.012 0.001 TYR A 424 PHE 0.016 0.001 PHE H 106 TRP 0.008 0.001 TRP A 606 HIS 0.004 0.001 HIS E 27 Details of bonding type rmsd covalent geometry : bond 0.00483 (16580) covalent geometry : angle 0.58655 (22494) SS BOND : bond 0.00433 ( 4) SS BOND : angle 5.99256 ( 8) hydrogen bonds : bond 0.03690 ( 948) hydrogen bonds : angle 4.48658 ( 2772) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3992 Ramachandran restraints generated. 1996 Oldfield, 0 Emsley, 1996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3992 Ramachandran restraints generated. 1996 Oldfield, 0 Emsley, 1996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 409 is missing expected H atoms. Skipping. Residue LYS 410 is missing expected H atoms. Skipping. Residue MET 414 is missing expected H atoms. Skipping. Residue LYS 439 is missing expected H atoms. Skipping. Residue LYS 441 is missing expected H atoms. Skipping. Residue LYS 449 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue LYS 506 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue LEU 540 is missing expected H atoms. Skipping. Residue LYS 697 is missing expected H atoms. Skipping. Residue LYS 699 is missing expected H atoms. Skipping. Residue SER 729 is missing expected H atoms. Skipping. Residue LYS 823 is missing expected H atoms. Skipping. Residue LYS 409 is missing expected H atoms. Skipping. Residue LYS 410 is missing expected H atoms. Skipping. Residue MET 414 is missing expected H atoms. Skipping. Residue LYS 439 is missing expected H atoms. Skipping. Residue LYS 441 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue THR 784 is missing expected H atoms. Skipping. Residue SER 785 is missing expected H atoms. Skipping. Residue SER 788 is missing expected H atoms. Skipping. Residue LEU 54 is missing expected H atoms. Skipping. Residue ILE 57 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue VAL 48 is missing expected H atoms. Skipping. Residue LEU 54 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue THR 127 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Residue LYS 409 is missing expected H atoms. Skipping. Residue LYS 410 is missing expected H atoms. Skipping. Residue MET 414 is missing expected H atoms. Skipping. Residue LYS 439 is missing expected H atoms. Skipping. Residue LYS 441 is missing expected H atoms. Skipping. Residue LYS 449 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue LYS 506 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue LEU 540 is missing expected H atoms. Skipping. Residue LYS 697 is missing expected H atoms. Skipping. Residue LYS 699 is missing expected H atoms. Skipping. Residue SER 729 is missing expected H atoms. Skipping. Residue LYS 823 is missing expected H atoms. Skipping. Residue LYS 409 is missing expected H atoms. Skipping. Residue LYS 410 is missing expected H atoms. Skipping. Residue MET 414 is missing expected H atoms. Skipping. Residue LYS 439 is missing expected H atoms. Skipping. Residue LYS 441 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue THR 784 is missing expected H atoms. Skipping. Residue SER 785 is missing expected H atoms. Skipping. Residue SER 788 is missing expected H atoms. Skipping. Residue LEU 54 is missing expected H atoms. Skipping. Residue ILE 57 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue VAL 48 is missing expected H atoms. Skipping. Residue LEU 54 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue THR 127 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Evaluate side-chains 245 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 232 time to evaluate : 0.888 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 705 GLU cc_start: 0.8217 (mm-30) cc_final: 0.8010 (mm-30) REVERT: B 713 GLU cc_start: 0.8626 (tt0) cc_final: 0.7947 (tm-30) REVERT: E 133 LYS cc_start: 0.6932 (mttm) cc_final: 0.6293 (tttm) REVERT: E 134 GLU cc_start: 0.7917 (tt0) cc_final: 0.7598 (tt0) REVERT: C 503 MET cc_start: 0.9367 (ttp) cc_final: 0.9027 (ttm) REVERT: D 713 GLU cc_start: 0.8681 (tt0) cc_final: 0.8012 (tm-30) REVERT: D 760 ASP cc_start: 0.8045 (p0) cc_final: 0.7645 (p0) REVERT: D 761 LYS cc_start: 0.9063 (tttt) cc_final: 0.8852 (tttt) REVERT: G 133 LYS cc_start: 0.7393 (mttm) cc_final: 0.7003 (tttm) REVERT: H 3 PHE cc_start: 0.7540 (OUTLIER) cc_final: 0.6594 (m-80) REVERT: H 22 PHE cc_start: 0.8547 (t80) cc_final: 0.8221 (t80) REVERT: H 138 LYS cc_start: 0.8313 (ttmm) cc_final: 0.7655 (mmpt) outliers start: 13 outliers final: 9 residues processed: 238 average time/residue: 0.2696 time to fit residues: 98.6114 Evaluate side-chains 209 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 199 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 504 ILE Chi-restraints excluded: chain F residue 25 ILE Chi-restraints excluded: chain F residue 38 PHE Chi-restraints excluded: chain F residue 89 LEU Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain C residue 504 ILE Chi-restraints excluded: chain H residue 3 PHE Chi-restraints excluded: chain H residue 21 ILE Chi-restraints excluded: chain H residue 38 PHE Chi-restraints excluded: chain H residue 95 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 5 optimal weight: 6.9990 chunk 69 optimal weight: 3.9990 chunk 127 optimal weight: 1.9990 chunk 44 optimal weight: 4.9990 chunk 34 optimal weight: 0.5980 chunk 130 optimal weight: 3.9990 chunk 123 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 180 optimal weight: 1.9990 chunk 128 optimal weight: 3.9990 chunk 24 optimal weight: 0.0980 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.109809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.089925 restraints weight = 115673.396| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 2.76 r_work: 0.3301 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.3130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 16584 Z= 0.172 Angle : 0.530 10.071 22502 Z= 0.283 Chirality : 0.061 1.722 2544 Planarity : 0.004 0.047 2698 Dihedral : 11.473 179.233 2636 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 0.86 % Allowed : 11.89 % Favored : 87.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.80 (0.19), residues: 1996 helix: 0.68 (0.14), residues: 1248 sheet: -2.56 (0.40), residues: 144 loop : -2.56 (0.24), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 59 TYR 0.009 0.001 TYR A 523 PHE 0.014 0.001 PHE H 106 TRP 0.007 0.001 TRP A 606 HIS 0.008 0.001 HIS G 75 Details of bonding type rmsd covalent geometry : bond 0.00385 (16580) covalent geometry : angle 0.52794 (22494) SS BOND : bond 0.00301 ( 4) SS BOND : angle 2.66716 ( 8) hydrogen bonds : bond 0.03561 ( 948) hydrogen bonds : angle 4.23449 ( 2772) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3992 Ramachandran restraints generated. 1996 Oldfield, 0 Emsley, 1996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3992 Ramachandran restraints generated. 1996 Oldfield, 0 Emsley, 1996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 409 is missing expected H atoms. Skipping. Residue LYS 410 is missing expected H atoms. Skipping. Residue MET 414 is missing expected H atoms. Skipping. Residue LYS 439 is missing expected H atoms. Skipping. Residue LYS 441 is missing expected H atoms. Skipping. Residue LYS 449 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue LYS 506 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue LEU 540 is missing expected H atoms. Skipping. Residue LYS 697 is missing expected H atoms. Skipping. Residue LYS 699 is missing expected H atoms. Skipping. Residue SER 729 is missing expected H atoms. Skipping. Residue LYS 823 is missing expected H atoms. Skipping. Residue LYS 409 is missing expected H atoms. Skipping. Residue LYS 410 is missing expected H atoms. Skipping. Residue MET 414 is missing expected H atoms. Skipping. Residue LYS 439 is missing expected H atoms. Skipping. Residue LYS 441 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue THR 784 is missing expected H atoms. Skipping. Residue SER 785 is missing expected H atoms. Skipping. Residue SER 788 is missing expected H atoms. Skipping. Residue LEU 54 is missing expected H atoms. Skipping. Residue ILE 57 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue VAL 48 is missing expected H atoms. Skipping. Residue LEU 54 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue THR 127 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Residue LYS 409 is missing expected H atoms. Skipping. Residue LYS 410 is missing expected H atoms. Skipping. Residue MET 414 is missing expected H atoms. Skipping. Residue LYS 439 is missing expected H atoms. Skipping. Residue LYS 441 is missing expected H atoms. Skipping. Residue LYS 449 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue LYS 506 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue LEU 540 is missing expected H atoms. Skipping. Residue LYS 697 is missing expected H atoms. Skipping. Residue LYS 699 is missing expected H atoms. Skipping. Residue SER 729 is missing expected H atoms. Skipping. Residue LYS 823 is missing expected H atoms. Skipping. Residue LYS 409 is missing expected H atoms. Skipping. Residue LYS 410 is missing expected H atoms. Skipping. Residue MET 414 is missing expected H atoms. Skipping. Residue LYS 439 is missing expected H atoms. Skipping. Residue LYS 441 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue THR 784 is missing expected H atoms. Skipping. Residue SER 785 is missing expected H atoms. Skipping. Residue SER 788 is missing expected H atoms. Skipping. Residue LEU 54 is missing expected H atoms. Skipping. Residue ILE 57 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue VAL 48 is missing expected H atoms. Skipping. Residue LEU 54 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue THR 127 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Evaluate side-chains 233 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 219 time to evaluate : 0.900 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 713 GLU cc_start: 0.8672 (tt0) cc_final: 0.8056 (tm-30) REVERT: E 133 LYS cc_start: 0.6948 (mttm) cc_final: 0.6217 (ttpp) REVERT: F 3 PHE cc_start: 0.7404 (OUTLIER) cc_final: 0.6909 (m-80) REVERT: F 81 MET cc_start: 0.7979 (ttm) cc_final: 0.7311 (ttm) REVERT: F 138 LYS cc_start: 0.8461 (ttmm) cc_final: 0.7482 (mmpt) REVERT: C 407 MET cc_start: 0.7235 (mtm) cc_final: 0.6509 (mtm) REVERT: C 503 MET cc_start: 0.9355 (ttp) cc_final: 0.8994 (ttm) REVERT: D 713 GLU cc_start: 0.8660 (tt0) cc_final: 0.8066 (tm-30) REVERT: G 133 LYS cc_start: 0.7438 (mttm) cc_final: 0.7041 (tttm) REVERT: H 3 PHE cc_start: 0.7647 (OUTLIER) cc_final: 0.6969 (m-80) REVERT: H 22 PHE cc_start: 0.8515 (t80) cc_final: 0.8160 (t80) REVERT: H 88 TRP cc_start: 0.8229 (m100) cc_final: 0.8021 (m100) REVERT: H 138 LYS cc_start: 0.8270 (ttmm) cc_final: 0.7638 (mmpt) REVERT: H 148 TYR cc_start: 0.8483 (t80) cc_final: 0.8206 (t80) outliers start: 14 outliers final: 10 residues processed: 227 average time/residue: 0.2905 time to fit residues: 100.2441 Evaluate side-chains 211 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 199 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 3 PHE Chi-restraints excluded: chain F residue 21 ILE Chi-restraints excluded: chain F residue 38 PHE Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain G residue 160 SER Chi-restraints excluded: chain H residue 3 PHE Chi-restraints excluded: chain H residue 21 ILE Chi-restraints excluded: chain H residue 28 ILE Chi-restraints excluded: chain H residue 38 PHE Chi-restraints excluded: chain H residue 89 LEU Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain H residue 136 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 6 optimal weight: 6.9990 chunk 44 optimal weight: 5.9990 chunk 0 optimal weight: 3.9990 chunk 30 optimal weight: 4.9990 chunk 7 optimal weight: 0.9980 chunk 149 optimal weight: 0.6980 chunk 186 optimal weight: 3.9990 chunk 196 optimal weight: 4.9990 chunk 48 optimal weight: 5.9990 chunk 185 optimal weight: 2.9990 chunk 171 optimal weight: 0.7980 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.108698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.086761 restraints weight = 114293.564| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 3.10 r_work: 0.3262 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.3579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 16584 Z= 0.187 Angle : 0.540 10.102 22502 Z= 0.285 Chirality : 0.061 1.710 2544 Planarity : 0.004 0.046 2698 Dihedral : 10.998 176.870 2636 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 1.47 % Allowed : 12.01 % Favored : 86.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.46 (0.19), residues: 1996 helix: 0.95 (0.15), residues: 1252 sheet: -2.55 (0.39), residues: 148 loop : -2.40 (0.24), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 628 TYR 0.010 0.001 TYR C 424 PHE 0.022 0.001 PHE D 541 TRP 0.007 0.001 TRP H 136 HIS 0.008 0.001 HIS E 75 Details of bonding type rmsd covalent geometry : bond 0.00418 (16580) covalent geometry : angle 0.54005 (22494) SS BOND : bond 0.00320 ( 4) SS BOND : angle 1.19688 ( 8) hydrogen bonds : bond 0.03483 ( 948) hydrogen bonds : angle 4.15272 ( 2772) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3992 Ramachandran restraints generated. 1996 Oldfield, 0 Emsley, 1996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3992 Ramachandran restraints generated. 1996 Oldfield, 0 Emsley, 1996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 409 is missing expected H atoms. Skipping. Residue LYS 410 is missing expected H atoms. Skipping. Residue MET 414 is missing expected H atoms. Skipping. Residue LYS 439 is missing expected H atoms. Skipping. Residue LYS 441 is missing expected H atoms. Skipping. Residue LYS 449 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue LYS 506 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue LEU 540 is missing expected H atoms. Skipping. Residue LYS 697 is missing expected H atoms. Skipping. Residue LYS 699 is missing expected H atoms. Skipping. Residue SER 729 is missing expected H atoms. Skipping. Residue LYS 823 is missing expected H atoms. Skipping. Residue LYS 409 is missing expected H atoms. Skipping. Residue LYS 410 is missing expected H atoms. Skipping. Residue MET 414 is missing expected H atoms. Skipping. Residue LYS 439 is missing expected H atoms. Skipping. Residue LYS 441 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue THR 784 is missing expected H atoms. Skipping. Residue SER 785 is missing expected H atoms. Skipping. Residue SER 788 is missing expected H atoms. Skipping. Residue LEU 54 is missing expected H atoms. Skipping. Residue ILE 57 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue VAL 48 is missing expected H atoms. Skipping. Residue LEU 54 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue THR 127 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Residue LYS 409 is missing expected H atoms. Skipping. Residue LYS 410 is missing expected H atoms. Skipping. Residue MET 414 is missing expected H atoms. Skipping. Residue LYS 439 is missing expected H atoms. Skipping. Residue LYS 441 is missing expected H atoms. Skipping. Residue LYS 449 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue LYS 506 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue LEU 540 is missing expected H atoms. Skipping. Residue LYS 697 is missing expected H atoms. Skipping. Residue LYS 699 is missing expected H atoms. Skipping. Residue SER 729 is missing expected H atoms. Skipping. Residue LYS 823 is missing expected H atoms. Skipping. Residue LYS 409 is missing expected H atoms. Skipping. Residue LYS 410 is missing expected H atoms. Skipping. Residue MET 414 is missing expected H atoms. Skipping. Residue LYS 439 is missing expected H atoms. Skipping. Residue LYS 441 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue THR 784 is missing expected H atoms. Skipping. Residue SER 785 is missing expected H atoms. Skipping. Residue SER 788 is missing expected H atoms. Skipping. Residue LEU 54 is missing expected H atoms. Skipping. Residue ILE 57 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue VAL 48 is missing expected H atoms. Skipping. Residue LEU 54 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue THR 127 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Evaluate side-chains 242 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 218 time to evaluate : 0.852 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 503 MET cc_start: 0.8483 (ttp) cc_final: 0.8275 (ptm) REVERT: B 713 GLU cc_start: 0.8711 (tt0) cc_final: 0.8092 (tm-30) REVERT: E 133 LYS cc_start: 0.6998 (mttm) cc_final: 0.6360 (tttm) REVERT: E 134 GLU cc_start: 0.8039 (tt0) cc_final: 0.7667 (tt0) REVERT: F 3 PHE cc_start: 0.7718 (OUTLIER) cc_final: 0.7158 (m-80) REVERT: F 81 MET cc_start: 0.8070 (ttm) cc_final: 0.7353 (ttm) REVERT: F 138 LYS cc_start: 0.8443 (ttmm) cc_final: 0.7485 (mmpt) REVERT: C 503 MET cc_start: 0.9366 (ttp) cc_final: 0.9004 (ttm) REVERT: D 713 GLU cc_start: 0.8702 (tt0) cc_final: 0.8109 (tm-30) REVERT: D 760 ASP cc_start: 0.8011 (p0) cc_final: 0.7618 (p0) REVERT: G 133 LYS cc_start: 0.7456 (mttm) cc_final: 0.7058 (tttm) REVERT: H 3 PHE cc_start: 0.7802 (OUTLIER) cc_final: 0.7163 (m-80) REVERT: H 138 LYS cc_start: 0.8323 (ttmm) cc_final: 0.7722 (mmpt) outliers start: 24 outliers final: 15 residues processed: 232 average time/residue: 0.2679 time to fit residues: 96.2873 Evaluate side-chains 214 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 197 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 504 ILE Chi-restraints excluded: chain E residue 160 SER Chi-restraints excluded: chain F residue 3 PHE Chi-restraints excluded: chain F residue 25 ILE Chi-restraints excluded: chain F residue 38 PHE Chi-restraints excluded: chain F residue 60 ILE Chi-restraints excluded: chain F residue 89 LEU Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain C residue 504 ILE Chi-restraints excluded: chain G residue 160 SER Chi-restraints excluded: chain H residue 3 PHE Chi-restraints excluded: chain H residue 21 ILE Chi-restraints excluded: chain H residue 28 ILE Chi-restraints excluded: chain H residue 38 PHE Chi-restraints excluded: chain H residue 89 LEU Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain H residue 136 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 57 optimal weight: 0.0170 chunk 54 optimal weight: 0.9990 chunk 152 optimal weight: 2.9990 chunk 122 optimal weight: 3.9990 chunk 120 optimal weight: 2.9990 chunk 150 optimal weight: 1.9990 chunk 149 optimal weight: 1.9990 chunk 170 optimal weight: 9.9990 chunk 19 optimal weight: 0.5980 chunk 194 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 overall best weight: 1.1224 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.109573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.087715 restraints weight = 114316.369| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 3.10 r_work: 0.3278 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.3813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16584 Z= 0.126 Angle : 0.499 10.038 22502 Z= 0.263 Chirality : 0.060 1.705 2544 Planarity : 0.003 0.046 2698 Dihedral : 10.344 169.458 2636 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 1.23 % Allowed : 12.99 % Favored : 85.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.19), residues: 1996 helix: 1.26 (0.15), residues: 1252 sheet: -2.27 (0.41), residues: 144 loop : -2.21 (0.25), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 104 TYR 0.007 0.001 TYR B 673 PHE 0.012 0.001 PHE A 546 TRP 0.006 0.001 TRP B 766 HIS 0.007 0.001 HIS E 75 Details of bonding type rmsd covalent geometry : bond 0.00279 (16580) covalent geometry : angle 0.49873 (22494) SS BOND : bond 0.00208 ( 4) SS BOND : angle 0.79752 ( 8) hydrogen bonds : bond 0.03292 ( 948) hydrogen bonds : angle 3.95778 ( 2772) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3992 Ramachandran restraints generated. 1996 Oldfield, 0 Emsley, 1996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3992 Ramachandran restraints generated. 1996 Oldfield, 0 Emsley, 1996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 409 is missing expected H atoms. Skipping. Residue LYS 410 is missing expected H atoms. Skipping. Residue MET 414 is missing expected H atoms. Skipping. Residue LYS 439 is missing expected H atoms. Skipping. Residue LYS 441 is missing expected H atoms. Skipping. Residue LYS 449 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue LYS 506 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue LEU 540 is missing expected H atoms. Skipping. Residue LYS 697 is missing expected H atoms. Skipping. Residue LYS 699 is missing expected H atoms. Skipping. Residue SER 729 is missing expected H atoms. Skipping. Residue LYS 823 is missing expected H atoms. Skipping. Residue LYS 409 is missing expected H atoms. Skipping. Residue LYS 410 is missing expected H atoms. Skipping. Residue MET 414 is missing expected H atoms. Skipping. Residue LYS 439 is missing expected H atoms. Skipping. Residue LYS 441 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue THR 784 is missing expected H atoms. Skipping. Residue SER 785 is missing expected H atoms. Skipping. Residue SER 788 is missing expected H atoms. Skipping. Residue LEU 54 is missing expected H atoms. Skipping. Residue ILE 57 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue VAL 48 is missing expected H atoms. Skipping. Residue LEU 54 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue THR 127 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Residue LYS 409 is missing expected H atoms. Skipping. Residue LYS 410 is missing expected H atoms. Skipping. Residue MET 414 is missing expected H atoms. Skipping. Residue LYS 439 is missing expected H atoms. Skipping. Residue LYS 441 is missing expected H atoms. Skipping. Residue LYS 449 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue LYS 506 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue LEU 540 is missing expected H atoms. Skipping. Residue LYS 697 is missing expected H atoms. Skipping. Residue LYS 699 is missing expected H atoms. Skipping. Residue SER 729 is missing expected H atoms. Skipping. Residue LYS 823 is missing expected H atoms. Skipping. Residue LYS 409 is missing expected H atoms. Skipping. Residue LYS 410 is missing expected H atoms. Skipping. Residue MET 414 is missing expected H atoms. Skipping. Residue LYS 439 is missing expected H atoms. Skipping. Residue LYS 441 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue THR 784 is missing expected H atoms. Skipping. Residue SER 785 is missing expected H atoms. Skipping. Residue SER 788 is missing expected H atoms. Skipping. Residue LEU 54 is missing expected H atoms. Skipping. Residue ILE 57 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue VAL 48 is missing expected H atoms. Skipping. Residue LEU 54 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue THR 127 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Evaluate side-chains 231 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 211 time to evaluate : 0.857 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 713 GLU cc_start: 0.8664 (tt0) cc_final: 0.8082 (tm-30) REVERT: E 133 LYS cc_start: 0.7037 (mttm) cc_final: 0.6279 (ttpp) REVERT: F 3 PHE cc_start: 0.7655 (OUTLIER) cc_final: 0.7125 (m-80) REVERT: F 138 LYS cc_start: 0.8407 (ttmm) cc_final: 0.8114 (tttt) REVERT: D 713 GLU cc_start: 0.8752 (tt0) cc_final: 0.8117 (tm-30) REVERT: G 133 LYS cc_start: 0.7464 (mttm) cc_final: 0.7096 (tttm) REVERT: H 3 PHE cc_start: 0.7812 (OUTLIER) cc_final: 0.7203 (m-80) REVERT: H 138 LYS cc_start: 0.8258 (ttmm) cc_final: 0.7724 (mmpt) outliers start: 20 outliers final: 17 residues processed: 224 average time/residue: 0.2786 time to fit residues: 95.9151 Evaluate side-chains 213 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 194 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 773 CYS Chi-restraints excluded: chain B residue 773 CYS Chi-restraints excluded: chain E residue 160 SER Chi-restraints excluded: chain F residue 3 PHE Chi-restraints excluded: chain F residue 21 ILE Chi-restraints excluded: chain F residue 25 ILE Chi-restraints excluded: chain F residue 38 PHE Chi-restraints excluded: chain F residue 60 ILE Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain C residue 773 CYS Chi-restraints excluded: chain D residue 773 CYS Chi-restraints excluded: chain G residue 160 SER Chi-restraints excluded: chain H residue 3 PHE Chi-restraints excluded: chain H residue 21 ILE Chi-restraints excluded: chain H residue 28 ILE Chi-restraints excluded: chain H residue 38 PHE Chi-restraints excluded: chain H residue 89 LEU Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain H residue 136 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 94 optimal weight: 2.9990 chunk 150 optimal weight: 1.9990 chunk 154 optimal weight: 1.9990 chunk 155 optimal weight: 0.5980 chunk 55 optimal weight: 1.9990 chunk 167 optimal weight: 4.9990 chunk 68 optimal weight: 4.9990 chunk 160 optimal weight: 3.9990 chunk 157 optimal weight: 3.9990 chunk 37 optimal weight: 6.9990 chunk 72 optimal weight: 1.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.108282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.088807 restraints weight = 114340.151| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 2.64 r_work: 0.3272 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.4075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 16584 Z= 0.172 Angle : 0.519 10.011 22502 Z= 0.276 Chirality : 0.061 1.710 2544 Planarity : 0.003 0.044 2698 Dihedral : 10.150 155.482 2636 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 1.53 % Allowed : 13.60 % Favored : 84.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.19), residues: 1996 helix: 1.33 (0.15), residues: 1252 sheet: -2.33 (0.40), residues: 148 loop : -2.18 (0.25), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 485 TYR 0.007 0.001 TYR C 424 PHE 0.014 0.001 PHE A 546 TRP 0.007 0.001 TRP H 103 HIS 0.008 0.001 HIS E 75 Details of bonding type rmsd covalent geometry : bond 0.00380 (16580) covalent geometry : angle 0.51839 (22494) SS BOND : bond 0.00279 ( 4) SS BOND : angle 0.92993 ( 8) hydrogen bonds : bond 0.03370 ( 948) hydrogen bonds : angle 4.00687 ( 2772) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3992 Ramachandran restraints generated. 1996 Oldfield, 0 Emsley, 1996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3992 Ramachandran restraints generated. 1996 Oldfield, 0 Emsley, 1996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 409 is missing expected H atoms. Skipping. Residue LYS 410 is missing expected H atoms. Skipping. Residue MET 414 is missing expected H atoms. Skipping. Residue LYS 439 is missing expected H atoms. Skipping. Residue LYS 441 is missing expected H atoms. Skipping. Residue LYS 449 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue LYS 506 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue LEU 540 is missing expected H atoms. Skipping. Residue LYS 697 is missing expected H atoms. Skipping. Residue LYS 699 is missing expected H atoms. Skipping. Residue SER 729 is missing expected H atoms. Skipping. Residue LYS 823 is missing expected H atoms. Skipping. Residue LYS 409 is missing expected H atoms. Skipping. Residue LYS 410 is missing expected H atoms. Skipping. Residue MET 414 is missing expected H atoms. Skipping. Residue LYS 439 is missing expected H atoms. Skipping. Residue LYS 441 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue THR 784 is missing expected H atoms. Skipping. Residue SER 785 is missing expected H atoms. Skipping. Residue SER 788 is missing expected H atoms. Skipping. Residue LEU 54 is missing expected H atoms. Skipping. Residue ILE 57 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue VAL 48 is missing expected H atoms. Skipping. Residue LEU 54 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue THR 127 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Residue LYS 409 is missing expected H atoms. Skipping. Residue LYS 410 is missing expected H atoms. Skipping. Residue MET 414 is missing expected H atoms. Skipping. Residue LYS 439 is missing expected H atoms. Skipping. Residue LYS 441 is missing expected H atoms. Skipping. Residue LYS 449 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue LYS 506 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue LEU 540 is missing expected H atoms. Skipping. Residue LYS 697 is missing expected H atoms. Skipping. Residue LYS 699 is missing expected H atoms. Skipping. Residue SER 729 is missing expected H atoms. Skipping. Residue LYS 823 is missing expected H atoms. Skipping. Residue LYS 409 is missing expected H atoms. Skipping. Residue LYS 410 is missing expected H atoms. Skipping. Residue MET 414 is missing expected H atoms. Skipping. Residue LYS 439 is missing expected H atoms. Skipping. Residue LYS 441 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue THR 784 is missing expected H atoms. Skipping. Residue SER 785 is missing expected H atoms. Skipping. Residue SER 788 is missing expected H atoms. Skipping. Residue LEU 54 is missing expected H atoms. Skipping. Residue ILE 57 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue VAL 48 is missing expected H atoms. Skipping. Residue LEU 54 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue THR 127 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Evaluate side-chains 224 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 199 time to evaluate : 0.893 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 713 GLU cc_start: 0.8652 (tt0) cc_final: 0.8074 (tm-30) REVERT: E 27 HIS cc_start: 0.8183 (OUTLIER) cc_final: 0.7835 (m-70) REVERT: E 133 LYS cc_start: 0.7110 (mttm) cc_final: 0.6470 (tttm) REVERT: F 3 PHE cc_start: 0.7737 (OUTLIER) cc_final: 0.7185 (m-80) REVERT: F 59 ARG cc_start: 0.6699 (ttp80) cc_final: 0.6369 (ttp80) REVERT: F 133 LYS cc_start: 0.6987 (mtpt) cc_final: 0.6787 (ttpt) REVERT: F 138 LYS cc_start: 0.8485 (ttmm) cc_final: 0.7609 (mmpt) REVERT: C 627 GLU cc_start: 0.8615 (mm-30) cc_final: 0.8396 (mm-30) REVERT: D 713 GLU cc_start: 0.8719 (tt0) cc_final: 0.8106 (tm-30) REVERT: D 760 ASP cc_start: 0.7971 (p0) cc_final: 0.7572 (p0) REVERT: G 133 LYS cc_start: 0.7482 (mttm) cc_final: 0.7048 (tttm) REVERT: G 134 GLU cc_start: 0.6570 (pt0) cc_final: 0.5947 (tt0) REVERT: H 3 PHE cc_start: 0.7906 (OUTLIER) cc_final: 0.7283 (m-80) REVERT: H 133 LYS cc_start: 0.6962 (mtpt) cc_final: 0.6760 (ttpt) REVERT: H 138 LYS cc_start: 0.8284 (ttmm) cc_final: 0.7757 (mmpt) outliers start: 25 outliers final: 20 residues processed: 215 average time/residue: 0.2739 time to fit residues: 91.4531 Evaluate side-chains 213 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 190 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 504 ILE Chi-restraints excluded: chain A residue 773 CYS Chi-restraints excluded: chain B residue 773 CYS Chi-restraints excluded: chain E residue 27 HIS Chi-restraints excluded: chain E residue 81 MET Chi-restraints excluded: chain E residue 160 SER Chi-restraints excluded: chain F residue 3 PHE Chi-restraints excluded: chain F residue 21 ILE Chi-restraints excluded: chain F residue 38 PHE Chi-restraints excluded: chain F residue 60 ILE Chi-restraints excluded: chain F residue 89 LEU Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain C residue 504 ILE Chi-restraints excluded: chain C residue 773 CYS Chi-restraints excluded: chain D residue 773 CYS Chi-restraints excluded: chain G residue 160 SER Chi-restraints excluded: chain H residue 3 PHE Chi-restraints excluded: chain H residue 21 ILE Chi-restraints excluded: chain H residue 28 ILE Chi-restraints excluded: chain H residue 38 PHE Chi-restraints excluded: chain H residue 89 LEU Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain H residue 136 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 184 optimal weight: 4.9990 chunk 1 optimal weight: 2.9990 chunk 188 optimal weight: 3.9990 chunk 168 optimal weight: 3.9990 chunk 123 optimal weight: 7.9990 chunk 198 optimal weight: 2.9990 chunk 39 optimal weight: 8.9990 chunk 29 optimal weight: 0.9980 chunk 33 optimal weight: 5.9990 chunk 71 optimal weight: 0.0970 chunk 64 optimal weight: 3.9990 overall best weight: 2.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.107036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.084958 restraints weight = 115717.084| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 3.10 r_work: 0.3227 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.4377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 16584 Z= 0.206 Angle : 0.547 10.278 22502 Z= 0.293 Chirality : 0.061 1.711 2544 Planarity : 0.004 0.042 2698 Dihedral : 9.590 130.884 2636 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 1.78 % Allowed : 14.22 % Favored : 84.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.19), residues: 1996 helix: 1.30 (0.15), residues: 1252 sheet: -2.28 (0.40), residues: 148 loop : -2.12 (0.25), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 628 TYR 0.009 0.001 TYR F 148 PHE 0.016 0.001 PHE H 106 TRP 0.008 0.001 TRP H 88 HIS 0.009 0.001 HIS E 75 Details of bonding type rmsd covalent geometry : bond 0.00457 (16580) covalent geometry : angle 0.54647 (22494) SS BOND : bond 0.00389 ( 4) SS BOND : angle 1.10275 ( 8) hydrogen bonds : bond 0.03530 ( 948) hydrogen bonds : angle 4.08742 ( 2772) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3992 Ramachandran restraints generated. 1996 Oldfield, 0 Emsley, 1996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3992 Ramachandran restraints generated. 1996 Oldfield, 0 Emsley, 1996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 409 is missing expected H atoms. Skipping. Residue LYS 410 is missing expected H atoms. Skipping. Residue MET 414 is missing expected H atoms. Skipping. Residue LYS 439 is missing expected H atoms. Skipping. Residue LYS 441 is missing expected H atoms. Skipping. Residue LYS 449 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue LYS 506 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue LEU 540 is missing expected H atoms. Skipping. Residue LYS 697 is missing expected H atoms. Skipping. Residue LYS 699 is missing expected H atoms. Skipping. Residue SER 729 is missing expected H atoms. Skipping. Residue LYS 823 is missing expected H atoms. Skipping. Residue LYS 409 is missing expected H atoms. Skipping. Residue LYS 410 is missing expected H atoms. Skipping. Residue MET 414 is missing expected H atoms. Skipping. Residue LYS 439 is missing expected H atoms. Skipping. Residue LYS 441 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue THR 784 is missing expected H atoms. Skipping. Residue SER 785 is missing expected H atoms. Skipping. Residue SER 788 is missing expected H atoms. Skipping. Residue LEU 54 is missing expected H atoms. Skipping. Residue ILE 57 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue VAL 48 is missing expected H atoms. Skipping. Residue LEU 54 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue THR 127 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Residue LYS 409 is missing expected H atoms. Skipping. Residue LYS 410 is missing expected H atoms. Skipping. Residue MET 414 is missing expected H atoms. Skipping. Residue LYS 439 is missing expected H atoms. Skipping. Residue LYS 441 is missing expected H atoms. Skipping. Residue LYS 449 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue LYS 506 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue LEU 540 is missing expected H atoms. Skipping. Residue LYS 697 is missing expected H atoms. Skipping. Residue LYS 699 is missing expected H atoms. Skipping. Residue SER 729 is missing expected H atoms. Skipping. Residue LYS 823 is missing expected H atoms. Skipping. Residue LYS 409 is missing expected H atoms. Skipping. Residue LYS 410 is missing expected H atoms. Skipping. Residue MET 414 is missing expected H atoms. Skipping. Residue LYS 439 is missing expected H atoms. Skipping. Residue LYS 441 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue THR 784 is missing expected H atoms. Skipping. Residue SER 785 is missing expected H atoms. Skipping. Residue SER 788 is missing expected H atoms. Skipping. Residue LEU 54 is missing expected H atoms. Skipping. Residue ILE 57 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue VAL 48 is missing expected H atoms. Skipping. Residue LEU 54 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue THR 127 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Evaluate side-chains 225 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 196 time to evaluate : 0.874 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 713 GLU cc_start: 0.8677 (tt0) cc_final: 0.8063 (tm-30) REVERT: B 760 ASP cc_start: 0.7904 (p0) cc_final: 0.7683 (p0) REVERT: E 133 LYS cc_start: 0.7144 (mttm) cc_final: 0.6518 (tttm) REVERT: F 3 PHE cc_start: 0.7946 (OUTLIER) cc_final: 0.7200 (m-80) REVERT: F 59 ARG cc_start: 0.6727 (ttp80) cc_final: 0.6395 (ttp80) REVERT: F 138 LYS cc_start: 0.8408 (ttmm) cc_final: 0.7471 (mmpt) REVERT: C 627 GLU cc_start: 0.8707 (mm-30) cc_final: 0.8493 (mm-30) REVERT: D 713 GLU cc_start: 0.8747 (tt0) cc_final: 0.8127 (tm-30) REVERT: D 760 ASP cc_start: 0.8055 (p0) cc_final: 0.7701 (p0) REVERT: G 71 GLU cc_start: 0.7479 (mp0) cc_final: 0.7219 (mp0) REVERT: G 75 HIS cc_start: 0.8173 (t70) cc_final: 0.7868 (t70) REVERT: G 133 LYS cc_start: 0.7499 (mttm) cc_final: 0.7105 (tttm) REVERT: H 3 PHE cc_start: 0.7994 (OUTLIER) cc_final: 0.7249 (m-80) REVERT: H 138 LYS cc_start: 0.8321 (ttmm) cc_final: 0.7781 (mmpt) outliers start: 29 outliers final: 20 residues processed: 214 average time/residue: 0.2637 time to fit residues: 87.7500 Evaluate side-chains 210 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 188 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 504 ILE Chi-restraints excluded: chain A residue 508 GLN Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 773 CYS Chi-restraints excluded: chain B residue 773 CYS Chi-restraints excluded: chain E residue 160 SER Chi-restraints excluded: chain F residue 3 PHE Chi-restraints excluded: chain F residue 38 PHE Chi-restraints excluded: chain F residue 60 ILE Chi-restraints excluded: chain F residue 89 LEU Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain C residue 508 GLN Chi-restraints excluded: chain C residue 773 CYS Chi-restraints excluded: chain D residue 773 CYS Chi-restraints excluded: chain G residue 160 SER Chi-restraints excluded: chain H residue 3 PHE Chi-restraints excluded: chain H residue 25 ILE Chi-restraints excluded: chain H residue 28 ILE Chi-restraints excluded: chain H residue 38 PHE Chi-restraints excluded: chain H residue 89 LEU Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain H residue 136 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 120 optimal weight: 4.9990 chunk 102 optimal weight: 6.9990 chunk 192 optimal weight: 6.9990 chunk 99 optimal weight: 0.7980 chunk 38 optimal weight: 6.9990 chunk 65 optimal weight: 4.9990 chunk 70 optimal weight: 9.9990 chunk 39 optimal weight: 2.9990 chunk 43 optimal weight: 0.8980 chunk 42 optimal weight: 4.9990 chunk 138 optimal weight: 5.9990 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.105758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.083646 restraints weight = 117359.767| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 3.05 r_work: 0.3229 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.4694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 16584 Z= 0.268 Angle : 0.595 10.076 22502 Z= 0.321 Chirality : 0.062 1.711 2544 Planarity : 0.004 0.040 2698 Dihedral : 9.355 107.669 2636 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.61 % Favored : 93.29 % Rotamer: Outliers : 2.02 % Allowed : 14.95 % Favored : 83.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.19), residues: 1996 helix: 1.12 (0.15), residues: 1252 sheet: -2.23 (0.40), residues: 158 loop : -2.14 (0.25), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 628 TYR 0.010 0.001 TYR C 523 PHE 0.020 0.002 PHE H 106 TRP 0.008 0.001 TRP H 103 HIS 0.008 0.001 HIS E 75 Details of bonding type rmsd covalent geometry : bond 0.00592 (16580) covalent geometry : angle 0.59463 (22494) SS BOND : bond 0.00392 ( 4) SS BOND : angle 1.33265 ( 8) hydrogen bonds : bond 0.03733 ( 948) hydrogen bonds : angle 4.25813 ( 2772) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3992 Ramachandran restraints generated. 1996 Oldfield, 0 Emsley, 1996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3992 Ramachandran restraints generated. 1996 Oldfield, 0 Emsley, 1996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 409 is missing expected H atoms. Skipping. Residue LYS 410 is missing expected H atoms. Skipping. Residue MET 414 is missing expected H atoms. Skipping. Residue LYS 439 is missing expected H atoms. Skipping. Residue LYS 441 is missing expected H atoms. Skipping. Residue LYS 449 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue LYS 506 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue LEU 540 is missing expected H atoms. Skipping. Residue LYS 697 is missing expected H atoms. Skipping. Residue LYS 699 is missing expected H atoms. Skipping. Residue SER 729 is missing expected H atoms. Skipping. Residue LYS 823 is missing expected H atoms. Skipping. Residue LYS 409 is missing expected H atoms. Skipping. Residue LYS 410 is missing expected H atoms. Skipping. Residue MET 414 is missing expected H atoms. Skipping. Residue LYS 439 is missing expected H atoms. Skipping. Residue LYS 441 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue THR 784 is missing expected H atoms. Skipping. Residue SER 785 is missing expected H atoms. Skipping. Residue SER 788 is missing expected H atoms. Skipping. Residue LEU 54 is missing expected H atoms. Skipping. Residue ILE 57 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue VAL 48 is missing expected H atoms. Skipping. Residue LEU 54 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue THR 127 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Residue LYS 409 is missing expected H atoms. Skipping. Residue LYS 410 is missing expected H atoms. Skipping. Residue MET 414 is missing expected H atoms. Skipping. Residue LYS 439 is missing expected H atoms. Skipping. Residue LYS 441 is missing expected H atoms. Skipping. Residue LYS 449 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue LYS 506 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue LEU 540 is missing expected H atoms. Skipping. Residue LYS 697 is missing expected H atoms. Skipping. Residue LYS 699 is missing expected H atoms. Skipping. Residue SER 729 is missing expected H atoms. Skipping. Residue LYS 823 is missing expected H atoms. Skipping. Residue LYS 409 is missing expected H atoms. Skipping. Residue LYS 410 is missing expected H atoms. Skipping. Residue MET 414 is missing expected H atoms. Skipping. Residue LYS 439 is missing expected H atoms. Skipping. Residue LYS 441 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue THR 784 is missing expected H atoms. Skipping. Residue SER 785 is missing expected H atoms. Skipping. Residue SER 788 is missing expected H atoms. Skipping. Residue LEU 54 is missing expected H atoms. Skipping. Residue ILE 57 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue VAL 48 is missing expected H atoms. Skipping. Residue LEU 54 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue THR 127 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Evaluate side-chains 228 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 195 time to evaluate : 0.812 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: 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 705 GLU cc_start: 0.8376 (mm-30) cc_final: 0.8156 (mm-30) REVERT: B 713 GLU cc_start: 0.8722 (tt0) cc_final: 0.8064 (tm-30) REVERT: B 760 ASP cc_start: 0.7992 (p0) cc_final: 0.7766 (p0) REVERT: E 133 LYS cc_start: 0.7211 (mttm) cc_final: 0.6680 (tttm) REVERT: F 3 PHE cc_start: 0.8025 (OUTLIER) cc_final: 0.7151 (m-80) REVERT: F 59 ARG cc_start: 0.6725 (ttp80) cc_final: 0.6393 (ttp80) REVERT: F 138 LYS cc_start: 0.8522 (ttmm) cc_final: 0.7618 (mmpt) REVERT: C 627 GLU cc_start: 0.8787 (mm-30) cc_final: 0.8583 (mm-30) REVERT: C 705 GLU cc_start: 0.8385 (mm-30) cc_final: 0.8168 (tp30) REVERT: D 713 GLU cc_start: 0.8774 (tt0) cc_final: 0.8168 (tm-30) REVERT: D 760 ASP cc_start: 0.8116 (p0) cc_final: 0.7789 (p0) REVERT: G 75 HIS cc_start: 0.8158 (t70) cc_final: 0.7881 (t70) REVERT: G 87 GLU cc_start: 0.8507 (tp30) cc_final: 0.8302 (tp30) REVERT: G 133 LYS cc_start: 0.7550 (mttm) cc_final: 0.7152 (tttm) REVERT: H 3 PHE cc_start: 0.8040 (OUTLIER) cc_final: 0.7072 (m-80) REVERT: H 138 LYS cc_start: 0.8344 (ttmm) cc_final: 0.7778 (mmpt) outliers start: 33 outliers final: 25 residues processed: 214 average time/residue: 0.2475 time to fit residues: 83.8882 Evaluate side-chains 218 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 191 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 508 GLN Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 773 CYS Chi-restraints excluded: chain B residue 649 THR Chi-restraints excluded: chain B residue 773 CYS Chi-restraints excluded: chain E residue 23 PHE Chi-restraints excluded: chain E residue 160 SER Chi-restraints excluded: chain F residue 3 PHE Chi-restraints excluded: chain F residue 25 ILE Chi-restraints excluded: chain F residue 38 PHE Chi-restraints excluded: chain F residue 60 ILE Chi-restraints excluded: chain F residue 89 LEU Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain C residue 508 GLN Chi-restraints excluded: chain C residue 604 VAL Chi-restraints excluded: chain C residue 649 THR Chi-restraints excluded: chain C residue 773 CYS Chi-restraints excluded: chain D residue 773 CYS Chi-restraints excluded: chain G residue 160 SER Chi-restraints excluded: chain H residue 3 PHE Chi-restraints excluded: chain H residue 25 ILE Chi-restraints excluded: chain H residue 28 ILE Chi-restraints excluded: chain H residue 38 PHE Chi-restraints excluded: chain H residue 89 LEU Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain H residue 97 LEU Chi-restraints excluded: chain H residue 136 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 87 optimal weight: 1.9990 chunk 169 optimal weight: 0.7980 chunk 99 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 100 optimal weight: 3.9990 chunk 71 optimal weight: 0.9980 chunk 23 optimal weight: 5.9990 chunk 199 optimal weight: 0.6980 chunk 144 optimal weight: 2.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.107130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.086390 restraints weight = 117265.190| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 3.00 r_work: 0.3251 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.4723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16584 Z= 0.143 Angle : 0.529 10.027 22502 Z= 0.278 Chirality : 0.061 1.701 2544 Planarity : 0.003 0.041 2698 Dihedral : 7.944 99.302 2636 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 1.59 % Allowed : 15.69 % Favored : 82.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.20), residues: 1996 helix: 1.41 (0.15), residues: 1258 sheet: -2.23 (0.42), residues: 148 loop : -2.12 (0.25), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 628 TYR 0.008 0.001 TYR H 10 PHE 0.012 0.001 PHE F 106 TRP 0.009 0.001 TRP H 103 HIS 0.007 0.001 HIS E 75 Details of bonding type rmsd covalent geometry : bond 0.00316 (16580) covalent geometry : angle 0.52888 (22494) SS BOND : bond 0.00148 ( 4) SS BOND : angle 1.00752 ( 8) hydrogen bonds : bond 0.03376 ( 948) hydrogen bonds : angle 3.94675 ( 2772) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3992 Ramachandran restraints generated. 1996 Oldfield, 0 Emsley, 1996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3992 Ramachandran restraints generated. 1996 Oldfield, 0 Emsley, 1996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 409 is missing expected H atoms. Skipping. Residue LYS 410 is missing expected H atoms. Skipping. Residue MET 414 is missing expected H atoms. Skipping. Residue LYS 439 is missing expected H atoms. Skipping. Residue LYS 441 is missing expected H atoms. Skipping. Residue LYS 449 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue LYS 506 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue LEU 540 is missing expected H atoms. Skipping. Residue LYS 697 is missing expected H atoms. Skipping. Residue LYS 699 is missing expected H atoms. Skipping. Residue SER 729 is missing expected H atoms. Skipping. Residue LYS 823 is missing expected H atoms. Skipping. Residue LYS 409 is missing expected H atoms. Skipping. Residue LYS 410 is missing expected H atoms. Skipping. Residue MET 414 is missing expected H atoms. Skipping. Residue LYS 439 is missing expected H atoms. Skipping. Residue LYS 441 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue THR 784 is missing expected H atoms. Skipping. Residue SER 785 is missing expected H atoms. Skipping. Residue SER 788 is missing expected H atoms. Skipping. Residue LEU 54 is missing expected H atoms. Skipping. Residue ILE 57 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue VAL 48 is missing expected H atoms. Skipping. Residue LEU 54 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue THR 127 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Residue LYS 409 is missing expected H atoms. Skipping. Residue LYS 410 is missing expected H atoms. Skipping. Residue MET 414 is missing expected H atoms. Skipping. Residue LYS 439 is missing expected H atoms. Skipping. Residue LYS 441 is missing expected H atoms. Skipping. Residue LYS 449 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue LYS 506 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue LEU 540 is missing expected H atoms. Skipping. Residue LYS 697 is missing expected H atoms. Skipping. Residue LYS 699 is missing expected H atoms. Skipping. Residue SER 729 is missing expected H atoms. Skipping. Residue LYS 823 is missing expected H atoms. Skipping. Residue LYS 409 is missing expected H atoms. Skipping. Residue LYS 410 is missing expected H atoms. Skipping. Residue MET 414 is missing expected H atoms. Skipping. Residue LYS 439 is missing expected H atoms. Skipping. Residue LYS 441 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue THR 784 is missing expected H atoms. Skipping. Residue SER 785 is missing expected H atoms. Skipping. Residue SER 788 is missing expected H atoms. Skipping. Residue LEU 54 is missing expected H atoms. Skipping. Residue ILE 57 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue VAL 48 is missing expected H atoms. Skipping. Residue LEU 54 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue THR 127 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Evaluate side-chains 231 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 205 time to evaluate : 0.848 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: symmetry clash 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: symmetry clash revert: symmetry clash REVERT: B 713 GLU cc_start: 0.8710 (tt0) cc_final: 0.8041 (tm-30) REVERT: B 760 ASP cc_start: 0.7991 (p0) cc_final: 0.7703 (p0) REVERT: E 133 LYS cc_start: 0.7217 (mttm) cc_final: 0.6606 (tttm) REVERT: F 59 ARG cc_start: 0.6691 (ttp80) cc_final: 0.6348 (ttp80) REVERT: C 705 GLU cc_start: 0.8365 (mm-30) cc_final: 0.8130 (tp30) REVERT: D 713 GLU cc_start: 0.8789 (tt0) cc_final: 0.8142 (tm-30) REVERT: D 760 ASP cc_start: 0.8038 (p0) cc_final: 0.7649 (p0) REVERT: G 75 HIS cc_start: 0.8112 (t70) cc_final: 0.7825 (t70) REVERT: G 133 LYS cc_start: 0.7476 (mttm) cc_final: 0.7147 (tttm) REVERT: H 25 ILE cc_start: 0.9356 (OUTLIER) cc_final: 0.9114 (mm) outliers start: 26 outliers final: 21 residues processed: 220 average time/residue: 0.2487 time to fit residues: 86.6878 Evaluate side-chains 224 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 202 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 508 GLN Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 773 CYS Chi-restraints excluded: chain B residue 649 THR Chi-restraints excluded: chain B residue 773 CYS Chi-restraints excluded: chain E residue 160 SER Chi-restraints excluded: chain F residue 38 PHE Chi-restraints excluded: chain F residue 60 ILE Chi-restraints excluded: chain F residue 89 LEU Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain C residue 508 GLN Chi-restraints excluded: chain C residue 649 THR Chi-restraints excluded: chain C residue 773 CYS Chi-restraints excluded: chain D residue 773 CYS Chi-restraints excluded: chain G residue 160 SER Chi-restraints excluded: chain H residue 25 ILE Chi-restraints excluded: chain H residue 28 ILE Chi-restraints excluded: chain H residue 38 PHE Chi-restraints excluded: chain H residue 89 LEU Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain H residue 97 LEU Chi-restraints excluded: chain H residue 136 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 45 optimal weight: 0.6980 chunk 94 optimal weight: 0.0020 chunk 197 optimal weight: 0.0980 chunk 85 optimal weight: 1.9990 chunk 151 optimal weight: 0.7980 chunk 192 optimal weight: 5.9990 chunk 166 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 149 optimal weight: 0.7980 chunk 3 optimal weight: 3.9990 chunk 77 optimal weight: 9.9990 overall best weight: 0.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.109001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.088914 restraints weight = 114895.770| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 2.93 r_work: 0.3287 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.4735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 16584 Z= 0.104 Angle : 0.503 10.008 22502 Z= 0.262 Chirality : 0.060 1.699 2544 Planarity : 0.003 0.041 2698 Dihedral : 6.257 68.540 2636 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 1.04 % Allowed : 16.24 % Favored : 82.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.20), residues: 1996 helix: 1.67 (0.15), residues: 1258 sheet: -2.02 (0.43), residues: 144 loop : -2.06 (0.25), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 59 TYR 0.007 0.001 TYR B 673 PHE 0.011 0.001 PHE A 546 TRP 0.008 0.001 TRP C 671 HIS 0.006 0.001 HIS E 75 Details of bonding type rmsd covalent geometry : bond 0.00227 (16580) covalent geometry : angle 0.50237 (22494) SS BOND : bond 0.00042 ( 4) SS BOND : angle 0.96396 ( 8) hydrogen bonds : bond 0.03156 ( 948) hydrogen bonds : angle 3.77403 ( 2772) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3992 Ramachandran restraints generated. 1996 Oldfield, 0 Emsley, 1996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3992 Ramachandran restraints generated. 1996 Oldfield, 0 Emsley, 1996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 409 is missing expected H atoms. Skipping. Residue LYS 410 is missing expected H atoms. Skipping. Residue MET 414 is missing expected H atoms. Skipping. Residue LYS 439 is missing expected H atoms. Skipping. Residue LYS 441 is missing expected H atoms. Skipping. Residue LYS 449 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue LYS 506 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue LEU 540 is missing expected H atoms. Skipping. Residue LYS 697 is missing expected H atoms. Skipping. Residue LYS 699 is missing expected H atoms. Skipping. Residue SER 729 is missing expected H atoms. Skipping. Residue LYS 823 is missing expected H atoms. Skipping. Residue LYS 409 is missing expected H atoms. Skipping. Residue LYS 410 is missing expected H atoms. Skipping. Residue MET 414 is missing expected H atoms. Skipping. Residue LYS 439 is missing expected H atoms. Skipping. Residue LYS 441 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue THR 784 is missing expected H atoms. Skipping. Residue SER 785 is missing expected H atoms. Skipping. Residue SER 788 is missing expected H atoms. Skipping. Residue LEU 54 is missing expected H atoms. Skipping. Residue ILE 57 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue VAL 48 is missing expected H atoms. Skipping. Residue LEU 54 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue THR 127 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Residue LYS 409 is missing expected H atoms. Skipping. Residue LYS 410 is missing expected H atoms. Skipping. Residue MET 414 is missing expected H atoms. Skipping. Residue LYS 439 is missing expected H atoms. Skipping. Residue LYS 441 is missing expected H atoms. Skipping. Residue LYS 449 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue LYS 506 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue LEU 540 is missing expected H atoms. Skipping. Residue LYS 697 is missing expected H atoms. Skipping. Residue LYS 699 is missing expected H atoms. Skipping. Residue SER 729 is missing expected H atoms. Skipping. Residue LYS 823 is missing expected H atoms. Skipping. Residue LYS 409 is missing expected H atoms. Skipping. Residue LYS 410 is missing expected H atoms. Skipping. Residue MET 414 is missing expected H atoms. Skipping. Residue LYS 439 is missing expected H atoms. Skipping. Residue LYS 441 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue THR 784 is missing expected H atoms. Skipping. Residue SER 785 is missing expected H atoms. Skipping. Residue SER 788 is missing expected H atoms. Skipping. Residue LEU 54 is missing expected H atoms. Skipping. Residue ILE 57 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue VAL 48 is missing expected H atoms. Skipping. Residue LEU 54 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue THR 127 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Evaluate side-chains 228 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 211 time to evaluate : 0.897 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: symmetry clash 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: symmetry clash REVERT: B 713 GLU cc_start: 0.8699 (tt0) cc_final: 0.8029 (tm-30) REVERT: B 760 ASP cc_start: 0.8057 (p0) cc_final: 0.7766 (p0) REVERT: E 133 LYS cc_start: 0.7338 (mttm) cc_final: 0.6601 (tttm) REVERT: F 59 ARG cc_start: 0.6750 (ttp80) cc_final: 0.6396 (ttp80) REVERT: C 627 GLU cc_start: 0.8678 (mm-30) cc_final: 0.8418 (mm-30) REVERT: C 705 GLU cc_start: 0.8358 (mm-30) cc_final: 0.8139 (tp30) REVERT: D 713 GLU cc_start: 0.8766 (tt0) cc_final: 0.8120 (tm-30) REVERT: G 75 HIS cc_start: 0.8065 (t70) cc_final: 0.7762 (t70) REVERT: G 133 LYS cc_start: 0.7550 (mttm) cc_final: 0.7063 (tttm) REVERT: H 25 ILE cc_start: 0.9345 (mt) cc_final: 0.9126 (mm) outliers start: 17 outliers final: 17 residues processed: 221 average time/residue: 0.2504 time to fit residues: 87.5617 Evaluate side-chains 220 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 203 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 508 GLN Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 773 CYS Chi-restraints excluded: chain B residue 773 CYS Chi-restraints excluded: chain E residue 160 SER Chi-restraints excluded: chain F residue 3 PHE Chi-restraints excluded: chain F residue 38 PHE Chi-restraints excluded: chain F residue 60 ILE Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain C residue 773 CYS Chi-restraints excluded: chain D residue 773 CYS Chi-restraints excluded: chain H residue 28 ILE Chi-restraints excluded: chain H residue 38 PHE Chi-restraints excluded: chain H residue 89 LEU Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain H residue 97 LEU Chi-restraints excluded: chain H residue 136 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 70 optimal weight: 10.0000 chunk 28 optimal weight: 3.9990 chunk 197 optimal weight: 5.9990 chunk 11 optimal weight: 3.9990 chunk 185 optimal weight: 3.9990 chunk 127 optimal weight: 0.8980 chunk 159 optimal weight: 3.9990 chunk 111 optimal weight: 1.9990 chunk 198 optimal weight: 1.9990 chunk 107 optimal weight: 4.9990 chunk 149 optimal weight: 0.5980 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.107569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.085521 restraints weight = 117287.491| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 3.08 r_work: 0.3262 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.4866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 16584 Z= 0.185 Angle : 0.527 9.984 22502 Z= 0.284 Chirality : 0.061 1.705 2544 Planarity : 0.003 0.039 2698 Dihedral : 6.042 59.182 2636 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 1.29 % Allowed : 16.42 % Favored : 82.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.20), residues: 1996 helix: 1.64 (0.15), residues: 1258 sheet: -1.95 (0.42), residues: 154 loop : -2.11 (0.25), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 694 TYR 0.010 0.001 TYR H 10 PHE 0.016 0.001 PHE H 106 TRP 0.012 0.001 TRP C 671 HIS 0.007 0.001 HIS E 75 Details of bonding type rmsd covalent geometry : bond 0.00412 (16580) covalent geometry : angle 0.52693 (22494) SS BOND : bond 0.00306 ( 4) SS BOND : angle 1.12980 ( 8) hydrogen bonds : bond 0.03358 ( 948) hydrogen bonds : angle 3.91900 ( 2772) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6867.94 seconds wall clock time: 117 minutes 35.43 seconds (7055.43 seconds total)