Starting phenix.real_space_refine on Sat Jun 28 02:16:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ud8_20734/06_2025/6ud8_20734_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ud8_20734/06_2025/6ud8_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6ud8_20734/06_2025/6ud8_20734.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ud8_20734/06_2025/6ud8_20734.map" model { file = "/net/cci-nas-00/data/ceres_data/6ud8_20734/06_2025/6ud8_20734_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ud8_20734/06_2025/6ud8_20734_trim.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2} 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: {'GLU:plan': 2, 'ARG:plan': 3, '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: {'GLU:plan': 1, 'ARG:plan': 3, 'HIS: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, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2} 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: {'GLU:plan': 2, 'ARG:plan': 3, '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: {'GLU:plan': 1, 'ARG:plan': 3, 'HIS: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: 14.08, per 1000 atoms: 0.44 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: 7.99 Conformation dependent library (CDL) restraints added in 2.3 seconds 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: 2.23 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: 10.76 Time building geometry restraints manager: 9.69 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: 0.09 Found NCS groups: ncs_group { reference = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'B' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'G' } ncs_group { reference = chain 'A' selection = chain 'C' } 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: 1.850 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: 0.520 Extract box with map and model: 1.210 Check model and map are aligned: 0.210 Set scattering table: 0.270 Process input model: 61.160 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.470 ------------------------------------------------------------------------------- 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 : 6.06 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.010 0.001 TRP A 606 HIS 0.004 0.001 HIS H 75 PHE 0.012 0.001 PHE A 546 TYR 0.015 0.001 TYR H 155 ARG 0.001 0.000 ARG B 628 Details of bonding type rmsd hydrogen bonds : bond 0.10787 ( 948) hydrogen bonds : angle 5.35005 ( 2772) SS BOND : bond 0.00260 ( 4) SS BOND : angle 0.52001 ( 8) covalent geometry : bond 0.00793 (16580) covalent geometry : angle 0.64449 (22494) *********************** 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 : 2.554 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: 0.7963 (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: 0.7280 (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: 0.7041 (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: 0.6377 time to fit residues: 331.3261 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 : 2.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 168 optimal weight: 3.9990 chunk 151 optimal weight: 0.6980 chunk 84 optimal weight: 0.9990 chunk 51 optimal weight: 0.5980 chunk 102 optimal weight: 10.0000 chunk 80 optimal weight: 0.6980 chunk 156 optimal weight: 3.9990 chunk 60 optimal weight: 4.9990 chunk 95 optimal weight: 1.9990 chunk 116 optimal weight: 0.5980 chunk 181 optimal weight: 3.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 764 ASN A 791 ASN B 791 ASN F 94 ASN C 764 ASN C 791 ASN D 791 ASN H 94 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.114769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.093379 restraints weight = 112702.408| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 3.18 r_work: 0.3391 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.2183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 16584 Z= 0.120 Angle : 0.522 10.366 22502 Z= 0.273 Chirality : 0.060 1.715 2544 Planarity : 0.004 0.059 2698 Dihedral : 12.382 176.554 2636 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 0.67 % Allowed : 9.01 % Favored : 90.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.18), residues: 1996 helix: 0.20 (0.14), residues: 1230 sheet: -2.87 (0.41), residues: 132 loop : -2.87 (0.23), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 606 HIS 0.004 0.001 HIS G 75 PHE 0.014 0.001 PHE A 546 TYR 0.010 0.001 TYR B 673 ARG 0.005 0.000 ARG H 59 Details of bonding type rmsd hydrogen bonds : bond 0.03525 ( 948) hydrogen bonds : angle 4.39547 ( 2772) SS BOND : bond 0.00274 ( 4) SS BOND : angle 4.01491 ( 8) covalent geometry : bond 0.00268 (16580) covalent geometry : angle 0.51610 (22494) *********************** 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 243 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 232 time to evaluate : 2.427 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: 0.8574 (tt0) cc_final: 0.7883 (tm-30) REVERT: E 133 LYS cc_start: 0.6845 (mttm) cc_final: 0.6106 (ttpp) REVERT: C 503 MET cc_start: 0.9394 (ttp) cc_final: 0.9049 (ttm) REVERT: D 713 GLU cc_start: 0.8668 (tt0) cc_final: 0.7905 (tm-30) REVERT: G 133 LYS cc_start: 0.7310 (mttm) cc_final: 0.6915 (tttm) REVERT: H 3 PHE cc_start: 0.7320 (OUTLIER) cc_final: 0.6223 (m-80) REVERT: H 22 PHE cc_start: 0.8446 (t80) cc_final: 0.8115 (t80) outliers start: 11 outliers final: 8 residues processed: 238 average time/residue: 0.6648 time to fit residues: 241.5423 Evaluate side-chains 216 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 207 time to evaluate : 2.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 504 ILE Chi-restraints excluded: chain E residue 4 THR Chi-restraints excluded: chain F residue 38 PHE 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 98 optimal weight: 3.9990 chunk 129 optimal weight: 0.6980 chunk 192 optimal weight: 4.9990 chunk 45 optimal weight: 0.9990 chunk 21 optimal weight: 5.9990 chunk 61 optimal weight: 3.9990 chunk 109 optimal weight: 0.9980 chunk 6 optimal weight: 6.9990 chunk 95 optimal weight: 0.0010 chunk 22 optimal weight: 0.9990 chunk 194 optimal weight: 2.9990 overall best weight: 0.7390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 756 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.114160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.092120 restraints weight = 114024.378| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 3.23 r_work: 0.3368 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.2658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 16584 Z= 0.113 Angle : 0.497 10.117 22502 Z= 0.260 Chirality : 0.060 1.717 2544 Planarity : 0.003 0.047 2698 Dihedral : 11.459 178.878 2636 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 0.43 % Allowed : 10.11 % Favored : 89.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.19), residues: 1996 helix: 0.91 (0.15), residues: 1232 sheet: -2.62 (0.41), residues: 132 loop : -2.41 (0.24), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 606 HIS 0.007 0.001 HIS G 75 PHE 0.013 0.001 PHE E 146 TYR 0.009 0.001 TYR A 421 ARG 0.004 0.000 ARG H 59 Details of bonding type rmsd hydrogen bonds : bond 0.03272 ( 948) hydrogen bonds : angle 4.11245 ( 2772) SS BOND : bond 0.00159 ( 4) SS BOND : angle 1.66606 ( 8) covalent geometry : bond 0.00243 (16580) covalent geometry : angle 0.49565 (22494) *********************** 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 226 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 219 time to evaluate : 3.338 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: A 407 MET cc_start: 0.6984 (mtm) cc_final: 0.6216 (mtm) REVERT: A 408 MET cc_start: 0.6870 (mmt) cc_final: 0.6225 (mmp) REVERT: B 713 GLU cc_start: 0.8608 (tt0) cc_final: 0.7912 (tm-30) REVERT: E 133 LYS cc_start: 0.6891 (mttm) cc_final: 0.6144 (ttpp) REVERT: F 3 PHE cc_start: 0.7062 (OUTLIER) cc_final: 0.6364 (m-80) REVERT: F 81 MET cc_start: 0.7750 (ttm) cc_final: 0.7076 (ttm) REVERT: F 148 TYR cc_start: 0.8565 (t80) cc_final: 0.7957 (t80) REVERT: C 503 MET cc_start: 0.9401 (ttp) cc_final: 0.8956 (ttm) REVERT: D 713 GLU cc_start: 0.8653 (tt0) cc_final: 0.7922 (tm-30) REVERT: G 133 LYS cc_start: 0.7324 (mttm) cc_final: 0.6909 (tttm) REVERT: H 3 PHE cc_start: 0.7202 (OUTLIER) cc_final: 0.6379 (m-80) REVERT: H 22 PHE cc_start: 0.8437 (t80) cc_final: 0.8116 (t80) REVERT: H 134 GLU cc_start: 0.8406 (tm-30) cc_final: 0.7535 (tt0) REVERT: H 138 LYS cc_start: 0.8246 (ttmm) cc_final: 0.7700 (mmpt) outliers start: 7 outliers final: 5 residues processed: 224 average time/residue: 0.6040 time to fit residues: 210.2114 Evaluate side-chains 204 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 197 time to evaluate : 2.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 3 PHE Chi-restraints excluded: chain F residue 38 PHE Chi-restraints excluded: chain F residue 95 VAL 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 45 optimal weight: 0.0770 chunk 58 optimal weight: 0.0010 chunk 184 optimal weight: 7.9990 chunk 147 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 100 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 chunk 174 optimal weight: 3.9990 chunk 102 optimal weight: 7.9990 chunk 117 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 overall best weight: 1.2150 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 756 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.112255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.089848 restraints weight = 114202.943| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 3.21 r_work: 0.3332 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.3042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 16584 Z= 0.136 Angle : 0.499 10.161 22502 Z= 0.262 Chirality : 0.060 1.719 2544 Planarity : 0.003 0.045 2698 Dihedral : 10.963 177.044 2636 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 1.16 % Allowed : 10.23 % Favored : 88.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.19), residues: 1996 helix: 1.27 (0.15), residues: 1224 sheet: -2.29 (0.41), residues: 140 loop : -2.26 (0.24), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 136 HIS 0.005 0.001 HIS G 75 PHE 0.013 0.001 PHE A 546 TYR 0.007 0.001 TYR A 424 ARG 0.002 0.000 ARG A 485 Details of bonding type rmsd hydrogen bonds : bond 0.03220 ( 948) hydrogen bonds : angle 4.00781 ( 2772) SS BOND : bond 0.00245 ( 4) SS BOND : angle 1.00679 ( 8) covalent geometry : bond 0.00306 (16580) covalent geometry : angle 0.49887 (22494) *********************** 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 233 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 214 time to evaluate : 3.339 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: A 408 MET cc_start: 0.6832 (mmt) cc_final: 0.6606 (mmp) REVERT: B 645 ILE cc_start: 0.8932 (pt) cc_final: 0.8699 (mt) REVERT: B 713 GLU cc_start: 0.8587 (tt0) cc_final: 0.7925 (tm-30) REVERT: E 133 LYS cc_start: 0.6892 (mttm) cc_final: 0.6152 (ttpp) REVERT: F 3 PHE cc_start: 0.7056 (OUTLIER) cc_final: 0.6434 (m-80) REVERT: F 81 MET cc_start: 0.7875 (ttm) cc_final: 0.7666 (ttm) REVERT: F 138 LYS cc_start: 0.8411 (ttmm) cc_final: 0.8108 (ttmt) REVERT: C 503 MET cc_start: 0.9398 (ttp) cc_final: 0.9052 (ttm) REVERT: D 496 MET cc_start: 0.8752 (ttm) cc_final: 0.8510 (ttm) REVERT: D 713 GLU cc_start: 0.8687 (tt0) cc_final: 0.8043 (tm-30) REVERT: G 133 LYS cc_start: 0.7414 (mttm) cc_final: 0.7015 (tttm) REVERT: H 3 PHE cc_start: 0.7304 (OUTLIER) cc_final: 0.6655 (m-80) REVERT: H 22 PHE cc_start: 0.8535 (t80) cc_final: 0.8231 (t80) REVERT: H 138 LYS cc_start: 0.8256 (ttmm) cc_final: 0.7677 (mmpt) outliers start: 19 outliers final: 14 residues processed: 223 average time/residue: 0.7680 time to fit residues: 273.0917 Evaluate side-chains 213 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 197 time to evaluate : 4.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 611 ILE Chi-restraints excluded: chain B residue 773 CYS 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 D residue 401 LEU Chi-restraints excluded: chain D residue 773 CYS Chi-restraints excluded: chain G residue 75 HIS 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 89 LEU Chi-restraints excluded: chain H residue 95 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 134 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 81 optimal weight: 0.9990 chunk 167 optimal weight: 4.9990 chunk 16 optimal weight: 0.9990 chunk 60 optimal weight: 4.9990 chunk 166 optimal weight: 1.9990 chunk 40 optimal weight: 5.9990 chunk 196 optimal weight: 5.9990 chunk 19 optimal weight: 4.9990 chunk 46 optimal weight: 0.7980 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 756 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.111041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.090055 restraints weight = 115656.817| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 3.02 r_work: 0.3315 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.3427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16584 Z= 0.143 Angle : 0.506 10.106 22502 Z= 0.265 Chirality : 0.060 1.714 2544 Planarity : 0.003 0.044 2698 Dihedral : 10.501 169.014 2636 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 1.47 % Allowed : 11.09 % Favored : 87.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.19), residues: 1996 helix: 1.42 (0.15), residues: 1228 sheet: -2.18 (0.42), residues: 140 loop : -2.17 (0.24), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 136 HIS 0.006 0.001 HIS E 27 PHE 0.026 0.001 PHE B 541 TYR 0.007 0.001 TYR C 424 ARG 0.002 0.000 ARG A 485 Details of bonding type rmsd hydrogen bonds : bond 0.03212 ( 948) hydrogen bonds : angle 3.94570 ( 2772) SS BOND : bond 0.00268 ( 4) SS BOND : angle 0.95253 ( 8) covalent geometry : bond 0.00319 (16580) covalent geometry : angle 0.50621 (22494) *********************** 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 233 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 209 time to evaluate : 2.530 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 713 GLU cc_start: 0.8677 (tt0) cc_final: 0.8029 (tm-30) REVERT: E 98 LEU cc_start: 0.9348 (tt) cc_final: 0.9111 (mt) REVERT: E 133 LYS cc_start: 0.6990 (mttm) cc_final: 0.6232 (ttpp) REVERT: F 3 PHE cc_start: 0.7216 (OUTLIER) cc_final: 0.6737 (m-80) REVERT: F 81 MET cc_start: 0.8037 (ttm) cc_final: 0.7295 (ttm) REVERT: F 138 LYS cc_start: 0.8380 (ttmm) cc_final: 0.8062 (tttt) REVERT: C 503 MET cc_start: 0.9376 (ttp) cc_final: 0.9012 (ttm) REVERT: D 496 MET cc_start: 0.8734 (ttm) cc_final: 0.8498 (ttm) REVERT: D 713 GLU cc_start: 0.8713 (tt0) cc_final: 0.8109 (tm-30) REVERT: G 133 LYS cc_start: 0.7453 (mttm) cc_final: 0.7083 (tttm) REVERT: H 3 PHE cc_start: 0.7475 (OUTLIER) cc_final: 0.6935 (m-80) REVERT: H 138 LYS cc_start: 0.8306 (ttmm) cc_final: 0.7766 (mmpt) outliers start: 24 outliers final: 14 residues processed: 226 average time/residue: 0.6471 time to fit residues: 231.3982 Evaluate side-chains 215 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 199 time to evaluate : 2.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 611 ILE Chi-restraints excluded: chain B residue 773 CYS 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 D residue 401 LEU Chi-restraints excluded: chain D residue 773 CYS 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 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 199 optimal weight: 3.9990 chunk 141 optimal weight: 8.9990 chunk 57 optimal weight: 3.9990 chunk 134 optimal weight: 1.9990 chunk 188 optimal weight: 0.9990 chunk 64 optimal weight: 0.9990 chunk 144 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 85 optimal weight: 4.9990 chunk 143 optimal weight: 0.9980 chunk 179 optimal weight: 2.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- 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 = 0.3799 r_free = 0.3799 target = 0.109830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.089065 restraints weight = 115610.698| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 3.15 r_work: 0.3292 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.3736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 16584 Z= 0.161 Angle : 0.505 10.088 22502 Z= 0.270 Chirality : 0.060 1.712 2544 Planarity : 0.003 0.043 2698 Dihedral : 10.038 152.811 2636 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 1.35 % Allowed : 12.56 % Favored : 86.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.19), residues: 1996 helix: 1.46 (0.15), residues: 1244 sheet: -2.21 (0.40), residues: 144 loop : -2.05 (0.25), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 136 HIS 0.007 0.001 HIS E 75 PHE 0.015 0.001 PHE A 546 TYR 0.006 0.001 TYR A 523 ARG 0.003 0.000 ARG B 628 Details of bonding type rmsd hydrogen bonds : bond 0.03273 ( 948) hydrogen bonds : angle 3.95337 ( 2772) SS BOND : bond 0.00272 ( 4) SS BOND : angle 0.99398 ( 8) covalent geometry : bond 0.00354 (16580) covalent geometry : angle 0.50468 (22494) *********************** 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 222 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 200 time to evaluate : 2.626 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: 0.8688 (tt0) cc_final: 0.8023 (tm-30) REVERT: E 133 LYS cc_start: 0.7023 (mttm) cc_final: 0.6277 (ttpp) REVERT: F 3 PHE cc_start: 0.7367 (OUTLIER) cc_final: 0.6861 (m-80) REVERT: D 496 MET cc_start: 0.8858 (ttm) cc_final: 0.8593 (ttm) REVERT: D 713 GLU cc_start: 0.8733 (tt0) cc_final: 0.8102 (tm-30) REVERT: G 133 LYS cc_start: 0.7453 (mttm) cc_final: 0.7019 (tttm) REVERT: H 3 PHE cc_start: 0.7687 (OUTLIER) cc_final: 0.7062 (m-80) outliers start: 22 outliers final: 17 residues processed: 214 average time/residue: 0.5381 time to fit residues: 181.6388 Evaluate side-chains 204 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 185 time to evaluate : 2.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain B residue 773 CYS Chi-restraints excluded: chain E residue 23 PHE 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 D residue 401 LEU Chi-restraints excluded: chain D residue 773 CYS Chi-restraints excluded: chain G residue 75 HIS 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 69 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 114 optimal weight: 1.9990 chunk 41 optimal weight: 7.9990 chunk 82 optimal weight: 0.5980 chunk 6 optimal weight: 6.9990 chunk 92 optimal weight: 6.9990 chunk 175 optimal weight: 0.6980 chunk 198 optimal weight: 2.9990 chunk 146 optimal weight: 3.9990 chunk 116 optimal weight: 0.9980 overall best weight: 1.4584 ------------------------------------------------------------------------------- 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 = 0.109732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.089018 restraints weight = 115558.811| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 3.13 r_work: 0.3296 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.3988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 16584 Z= 0.149 Angle : 0.504 10.109 22502 Z= 0.267 Chirality : 0.060 1.702 2544 Planarity : 0.003 0.042 2698 Dihedral : 9.199 127.482 2636 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 1.23 % Allowed : 13.42 % Favored : 85.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.20), residues: 1996 helix: 1.51 (0.15), residues: 1252 sheet: -2.12 (0.41), residues: 144 loop : -1.94 (0.25), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 103 HIS 0.007 0.001 HIS E 75 PHE 0.014 0.001 PHE A 546 TYR 0.007 0.001 TYR D 421 ARG 0.002 0.000 ARG A 485 Details of bonding type rmsd hydrogen bonds : bond 0.03236 ( 948) hydrogen bonds : angle 3.89284 ( 2772) SS BOND : bond 0.00275 ( 4) SS BOND : angle 0.95190 ( 8) covalent geometry : bond 0.00330 (16580) covalent geometry : angle 0.50413 (22494) *********************** 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 217 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 197 time to evaluate : 2.621 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: B 713 GLU cc_start: 0.8686 (tt0) cc_final: 0.8018 (tm-30) REVERT: E 133 LYS cc_start: 0.7069 (mttm) cc_final: 0.6289 (ttpp) REVERT: F 3 PHE cc_start: 0.7609 (OUTLIER) cc_final: 0.7083 (m-80) REVERT: F 138 LYS cc_start: 0.8421 (ttmm) cc_final: 0.8142 (tttt) REVERT: D 713 GLU cc_start: 0.8756 (tt0) cc_final: 0.8123 (tm-30) REVERT: G 133 LYS cc_start: 0.7421 (mttm) cc_final: 0.6992 (tttm) REVERT: H 3 PHE cc_start: 0.7796 (OUTLIER) cc_final: 0.7106 (m-80) REVERT: H 138 LYS cc_start: 0.8242 (ttmm) cc_final: 0.7718 (mmpt) outliers start: 20 outliers final: 17 residues processed: 208 average time/residue: 0.5227 time to fit residues: 172.5779 Evaluate side-chains 212 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 193 time to evaluate : 2.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain B residue 773 CYS Chi-restraints excluded: chain E residue 23 PHE 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 D residue 773 CYS Chi-restraints excluded: chain G residue 75 HIS 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 75 optimal weight: 2.9990 chunk 197 optimal weight: 7.9990 chunk 43 optimal weight: 1.9990 chunk 155 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 chunk 195 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 34 optimal weight: 0.0170 chunk 169 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 overall best weight: 1.6026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 756 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.109025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.088191 restraints weight = 116199.286| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 3.14 r_work: 0.3270 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.4188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 16584 Z= 0.160 Angle : 0.509 10.214 22502 Z= 0.272 Chirality : 0.060 1.699 2544 Planarity : 0.003 0.041 2698 Dihedral : 8.324 105.147 2636 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 1.47 % Allowed : 13.30 % Favored : 85.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.20), residues: 1996 helix: 1.55 (0.15), residues: 1252 sheet: -2.05 (0.41), residues: 144 loop : -1.92 (0.26), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 136 HIS 0.008 0.001 HIS E 75 PHE 0.015 0.001 PHE C 546 TYR 0.006 0.001 TYR A 424 ARG 0.002 0.000 ARG A 485 Details of bonding type rmsd hydrogen bonds : bond 0.03276 ( 948) hydrogen bonds : angle 3.91349 ( 2772) SS BOND : bond 0.00224 ( 4) SS BOND : angle 1.03900 ( 8) covalent geometry : bond 0.00354 (16580) covalent geometry : angle 0.50838 (22494) *********************** 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 220 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 196 time to evaluate : 2.602 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: 0.8678 (tt0) cc_final: 0.8010 (tm-30) REVERT: B 760 ASP cc_start: 0.8010 (p0) cc_final: 0.7738 (p0) REVERT: E 133 LYS cc_start: 0.7095 (mttm) cc_final: 0.6347 (tttm) REVERT: F 3 PHE cc_start: 0.7721 (OUTLIER) cc_final: 0.7166 (m-80) REVERT: F 138 LYS cc_start: 0.8422 (ttmm) cc_final: 0.8134 (tttt) REVERT: D 713 GLU cc_start: 0.8750 (tt0) cc_final: 0.8121 (tm-30) REVERT: D 760 ASP cc_start: 0.8021 (p0) cc_final: 0.7694 (p0) REVERT: G 133 LYS cc_start: 0.7423 (mttm) cc_final: 0.6996 (tttm) REVERT: H 3 PHE cc_start: 0.7880 (OUTLIER) cc_final: 0.7172 (m-80) outliers start: 24 outliers final: 19 residues processed: 209 average time/residue: 0.5829 time to fit residues: 191.4611 Evaluate side-chains 208 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 187 time to evaluate : 2.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 508 GLN Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain B residue 773 CYS Chi-restraints excluded: chain E residue 23 PHE 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 D residue 401 LEU Chi-restraints excluded: chain D residue 773 CYS Chi-restraints excluded: chain G residue 75 HIS 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 137 optimal weight: 6.9990 chunk 138 optimal weight: 0.8980 chunk 85 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 150 optimal weight: 1.9990 chunk 76 optimal weight: 3.9990 chunk 122 optimal weight: 0.9980 chunk 84 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 66 optimal weight: 0.9990 chunk 177 optimal weight: 9.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- 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 = 0.3792 r_free = 0.3792 target = 0.109634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.088849 restraints weight = 115234.066| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 3.15 r_work: 0.3287 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.4322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16584 Z= 0.129 Angle : 0.498 10.021 22502 Z= 0.264 Chirality : 0.060 1.709 2544 Planarity : 0.003 0.042 2698 Dihedral : 7.851 102.694 2636 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 1.53 % Allowed : 13.42 % Favored : 85.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.20), residues: 1996 helix: 1.68 (0.15), residues: 1258 sheet: -1.82 (0.41), residues: 154 loop : -1.94 (0.26), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 766 HIS 0.007 0.001 HIS E 75 PHE 0.013 0.001 PHE A 546 TYR 0.006 0.001 TYR H 105 ARG 0.002 0.000 ARG E 104 Details of bonding type rmsd hydrogen bonds : bond 0.03184 ( 948) hydrogen bonds : angle 3.83383 ( 2772) SS BOND : bond 0.00182 ( 4) SS BOND : angle 0.94171 ( 8) covalent geometry : bond 0.00285 (16580) covalent geometry : angle 0.49809 (22494) *********************** 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 225 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 200 time to evaluate : 2.471 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: B 713 GLU cc_start: 0.8664 (tt0) cc_final: 0.7986 (tm-30) REVERT: E 133 LYS cc_start: 0.7132 (mttm) cc_final: 0.6350 (tttm) REVERT: F 3 PHE cc_start: 0.7752 (OUTLIER) cc_final: 0.7184 (m-80) REVERT: F 59 ARG cc_start: 0.6758 (ttp80) cc_final: 0.6446 (ttp80) REVERT: F 138 LYS cc_start: 0.8400 (ttmm) cc_final: 0.8123 (tttt) REVERT: D 713 GLU cc_start: 0.8743 (tt0) cc_final: 0.8114 (tm-30) REVERT: D 760 ASP cc_start: 0.8003 (p0) cc_final: 0.7664 (p0) REVERT: G 71 GLU cc_start: 0.7508 (mp0) cc_final: 0.7260 (mp0) REVERT: G 133 LYS cc_start: 0.7416 (mttm) cc_final: 0.6989 (tttm) REVERT: H 3 PHE cc_start: 0.7878 (OUTLIER) cc_final: 0.7182 (m-80) outliers start: 25 outliers final: 22 residues processed: 212 average time/residue: 0.5959 time to fit residues: 202.7012 Evaluate side-chains 216 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 192 time to evaluate : 2.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 508 GLN Chi-restraints excluded: chain A residue 610 LEU 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 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 805 LEU Chi-restraints excluded: chain D residue 401 LEU Chi-restraints excluded: chain D residue 773 CYS Chi-restraints excluded: chain G residue 75 HIS 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 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 102 optimal weight: 6.9990 chunk 199 optimal weight: 2.9990 chunk 180 optimal weight: 3.9990 chunk 120 optimal weight: 0.9980 chunk 33 optimal weight: 7.9990 chunk 194 optimal weight: 0.7980 chunk 111 optimal weight: 0.9980 chunk 89 optimal weight: 3.9990 chunk 76 optimal weight: 4.9990 chunk 51 optimal weight: 0.6980 chunk 189 optimal weight: 2.9990 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 508 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.109277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.087366 restraints weight = 115503.951| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 3.10 r_work: 0.3285 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.4435 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= 0.140 Angle : 0.504 10.118 22502 Z= 0.268 Chirality : 0.060 1.701 2544 Planarity : 0.003 0.040 2698 Dihedral : 7.737 104.633 2636 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 1.47 % Allowed : 13.79 % Favored : 84.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.20), residues: 1996 helix: 1.73 (0.15), residues: 1258 sheet: -1.79 (0.43), residues: 144 loop : -1.90 (0.26), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 103 HIS 0.008 0.001 HIS E 75 PHE 0.014 0.001 PHE C 546 TYR 0.006 0.001 TYR H 10 ARG 0.002 0.000 ARG A 485 Details of bonding type rmsd hydrogen bonds : bond 0.03186 ( 948) hydrogen bonds : angle 3.84405 ( 2772) SS BOND : bond 0.00164 ( 4) SS BOND : angle 1.00898 ( 8) covalent geometry : bond 0.00310 (16580) covalent geometry : angle 0.50402 (22494) ********************** 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 220 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 196 time to evaluate : 2.395 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: 0.8655 (tt0) cc_final: 0.8013 (tm-30) REVERT: E 133 LYS cc_start: 0.7271 (mttm) cc_final: 0.6414 (tttm) REVERT: F 3 PHE cc_start: 0.7851 (OUTLIER) cc_final: 0.7283 (m-80) REVERT: F 59 ARG cc_start: 0.6766 (ttp80) cc_final: 0.6450 (ttp80) REVERT: F 138 LYS cc_start: 0.8419 (ttmm) cc_final: 0.7582 (mmpt) REVERT: D 713 GLU cc_start: 0.8744 (tt0) cc_final: 0.8130 (tm-30) REVERT: D 760 ASP cc_start: 0.7971 (p0) cc_final: 0.7634 (p0) REVERT: G 71 GLU cc_start: 0.7522 (mp0) cc_final: 0.7250 (mp0) REVERT: G 133 LYS cc_start: 0.7488 (mttm) cc_final: 0.6996 (tttm) REVERT: H 3 PHE cc_start: 0.7883 (OUTLIER) cc_final: 0.7223 (m-80) outliers start: 24 outliers final: 21 residues processed: 207 average time/residue: 0.5488 time to fit residues: 178.9858 Evaluate side-chains 214 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 191 time to evaluate : 2.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 508 GLN Chi-restraints excluded: chain A residue 610 LEU 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 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 D residue 401 LEU Chi-restraints excluded: chain D residue 773 CYS Chi-restraints excluded: chain G residue 75 HIS 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 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 13 optimal weight: 0.8980 chunk 15 optimal weight: 3.9990 chunk 189 optimal weight: 4.9990 chunk 66 optimal weight: 0.6980 chunk 132 optimal weight: 2.9990 chunk 157 optimal weight: 0.7980 chunk 188 optimal weight: 0.7980 chunk 81 optimal weight: 3.9990 chunk 159 optimal weight: 4.9990 chunk 186 optimal weight: 3.9990 chunk 20 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3800 r_free = 0.3800 target = 0.110101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.088348 restraints weight = 115407.045| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 3.12 r_work: 0.3298 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.4522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 16584 Z= 0.110 Angle : 0.495 10.051 22502 Z= 0.259 Chirality : 0.060 1.702 2544 Planarity : 0.003 0.040 2698 Dihedral : 7.303 101.014 2636 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 1.41 % Allowed : 14.15 % Favored : 84.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.20), residues: 1996 helix: 1.87 (0.15), residues: 1258 sheet: -1.64 (0.42), residues: 154 loop : -1.86 (0.26), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 103 HIS 0.006 0.001 HIS E 75 PHE 0.016 0.001 PHE H 22 TYR 0.007 0.001 TYR B 673 ARG 0.005 0.000 ARG B 694 Details of bonding type rmsd hydrogen bonds : bond 0.03072 ( 948) hydrogen bonds : angle 3.75324 ( 2772) SS BOND : bond 0.00095 ( 4) SS BOND : angle 0.93249 ( 8) covalent geometry : bond 0.00242 (16580) covalent geometry : angle 0.49515 (22494) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14661.67 seconds wall clock time: 257 minutes 32.11 seconds (15452.11 seconds total)