Starting phenix.real_space_refine on Fri Mar 6 16:10:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ud4_20733/03_2026/6ud4_20733_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ud4_20733/03_2026/6ud4_20733.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6ud4_20733/03_2026/6ud4_20733.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ud4_20733/03_2026/6ud4_20733.map" model { file = "/net/cci-nas-00/data/ceres_data/6ud4_20733/03_2026/6ud4_20733_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ud4_20733/03_2026/6ud4_20733_trim.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians P 4 5.49 5 S 120 5.16 5 C 10673 2.51 5 N 2519 2.21 5 O 2844 1.98 5 F 12 1.80 5 H 15470 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 72 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 31642 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 5658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 378, 5658 Classifications: {'peptide': 378} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 366} Chain breaks: 2 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 92 Unresolved non-hydrogen angles: 105 Unresolved non-hydrogen dihedrals: 80 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 4, 'ASN:plan1': 2, 'ASP:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 40 Chain: "B" Number of atoms: 5731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 378, 5731 Classifications: {'peptide': 378} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 366} Chain breaks: 2 Unresolved non-hydrogen bonds: 65 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 57 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: 2112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 2112 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 3, 'TRANS': 128} Chain breaks: 2 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 3, 'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 26 Chain: "F" Number of atoms: 2147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 2147 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 2, 'TRANS': 131} Chain breaks: 2 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'HIS:plan': 1, 'ARG:plan': 3, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "G" Number of atoms: 2121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 2121 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 3, 'TRANS': 128} Chain breaks: 2 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 3, 'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 26 Chain: "H" Number of atoms: 2147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 2147 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 2, 'TRANS': 131} Chain breaks: 2 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'HIS:plan': 1, 'ARG:plan': 3, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "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: 86 Unresolved non-hydrogen angles: 98 Unresolved non-hydrogen dihedrals: 75 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 4, 'ASN:plan1': 2, 'ASP:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 35 Chain: "D" Number of atoms: 5731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 378, 5731 Classifications: {'peptide': 378} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 366} Chain breaks: 2 Unresolved non-hydrogen bonds: 65 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 57 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: "A" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 80 Unusual residues: {'CLR': 1, 'OLC': 1, 'ZK1': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} 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: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 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} 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} Time building chain proxies: 6.53, per 1000 atoms: 0.21 Number of scatterers: 31642 At special positions: 0 Unit cell: (118.326, 101.27, 147.108, 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 2844 8.00 N 2519 7.00 C 10673 6.00 H 15470 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 718 " - pdb=" SG CYS A 773 " distance=2.03 Simple disulfide: pdb=" SG CYS B 718 " - pdb=" SG CYS B 773 " distance=2.03 Simple disulfide: pdb=" SG CYS C 718 " - pdb=" SG CYS C 773 " distance=2.03 Simple disulfide: pdb=" SG CYS D 718 " - pdb=" SG CYS D 773 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.07 Conformation dependent library (CDL) restraints added in 1.0 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 20 sheets defined 63.1% alpha, 5.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.76 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: 4.068A 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: 4.003A pdb=" N GLY A 689 " --> pdb=" O THR A 685 " (cutoff:3.500A) Processing helix chain 'A' and resid 706 through 714 Processing helix chain 'A' and resid 741 through 756 removed outlier: 4.139A pdb=" N LEU A 748 " --> pdb=" O ASN A 744 " (cutoff:3.500A) removed outlier: 4.177A 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: 3.548A pdb=" N PHE A 796 " --> pdb=" O VAL A 792 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ALA A 820 " --> pdb=" O TYR A 816 " (cutoff:3.500A) Processing helix chain 'B' and resid 423 through 437 removed outlier: 3.659A 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 487 Processing helix chain 'B' and resid 522 through 546 removed outlier: 3.660A pdb=" N SER B 544 " --> pdb=" O LEU B 540 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ARG B 545 " --> pdb=" O PHE B 541 " (cutoff:3.500A) Processing helix chain 'B' and resid 599 through 627 removed outlier: 3.693A pdb=" N VAL B 626 " --> pdb=" O ALA B 622 " (cutoff:3.500A) Processing helix chain 'B' and resid 635 through 642 removed outlier: 4.090A pdb=" N LEU B 639 " --> pdb=" O SER B 635 " (cutoff:3.500A) Processing helix chain 'B' and resid 653 through 661 removed outlier: 3.526A pdb=" N GLU B 657 " --> pdb=" O GLY B 653 " (cutoff:3.500A) Processing helix chain 'B' and resid 666 through 676 Processing helix chain 'B' and resid 685 through 696 Processing helix chain 'B' and resid 706 through 715 Processing helix chain 'B' and resid 741 through 757 removed outlier: 4.664A pdb=" N ALA B 745 " --> pdb=" O SER B 741 " (cutoff:3.500A) removed outlier: 3.914A 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: 3.660A pdb=" N PHE B 796 " --> pdb=" O VAL B 792 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ARG B 819 " --> pdb=" O CYS B 815 " (cutoff:3.500A) Processing helix chain 'E' and resid 5 through 35 removed outlier: 3.878A pdb=" N CYS E 9 " --> pdb=" O PHE E 5 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ALA E 19 " --> pdb=" O VAL E 15 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N PHE E 22 " --> pdb=" O ALA E 18 " (cutoff:3.500A) Processing helix chain 'E' and resid 51 through 67 removed outlier: 4.036A pdb=" N ILE E 60 " --> pdb=" O ASN E 56 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU E 63 " --> pdb=" O ARG E 59 " (cutoff:3.500A) Processing helix chain 'E' and resid 67 through 85 removed outlier: 4.518A pdb=" N GLU E 71 " --> pdb=" O LEU E 67 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N TYR E 72 " --> pdb=" O VAL E 68 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 92 Processing helix chain 'E' and resid 94 through 107 Processing helix chain 'E' and resid 128 through 158 removed outlier: 3.710A pdb=" N PHE E 147 " --> pdb=" O LEU E 143 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL E 158 " --> pdb=" O ILE E 154 " (cutoff:3.500A) Processing helix chain 'F' and resid 5 through 38 removed outlier: 3.793A pdb=" N CYS F 9 " --> pdb=" O PHE F 5 " (cutoff:3.500A) removed outlier: 3.707A 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: 3.758A pdb=" N TYR F 72 " --> pdb=" O VAL F 68 " (cutoff:3.500A) Processing helix chain 'F' and resid 90 through 105 Proline residue: F 96 - end of helix removed outlier: 4.023A pdb=" N TYR F 105 " --> pdb=" O HIS F 101 " (cutoff:3.500A) Processing helix chain 'F' and resid 126 through 158 removed outlier: 4.048A pdb=" N TYR F 130 " --> pdb=" O ASP F 126 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N LYS F 133 " --> pdb=" O SER F 129 " (cutoff:3.500A) Processing helix chain 'G' and resid 5 through 35 removed outlier: 3.878A pdb=" N CYS G 9 " --> pdb=" O PHE G 5 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ALA G 19 " --> pdb=" O VAL G 15 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N PHE G 22 " --> pdb=" O ALA G 18 " (cutoff:3.500A) Processing helix chain 'G' and resid 51 through 67 removed outlier: 4.036A pdb=" N ILE G 60 " --> pdb=" O ASN G 56 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU G 63 " --> pdb=" O ARG G 59 " (cutoff:3.500A) Processing helix chain 'G' and resid 67 through 85 removed outlier: 4.518A pdb=" N GLU G 71 " --> pdb=" O LEU G 67 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N TYR G 72 " --> pdb=" O VAL G 68 " (cutoff:3.500A) Processing helix chain 'G' and resid 87 through 92 Processing helix chain 'G' and resid 94 through 107 Processing helix chain 'G' and resid 128 through 158 removed outlier: 3.710A pdb=" N PHE G 147 " --> pdb=" O LEU G 143 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL G 158 " --> pdb=" O ILE G 154 " (cutoff:3.500A) Processing helix chain 'H' and resid 5 through 38 removed outlier: 3.793A pdb=" N CYS H 9 " --> pdb=" O PHE H 5 " (cutoff:3.500A) removed outlier: 3.706A 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: 3.759A pdb=" N TYR H 72 " --> pdb=" O VAL H 68 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 105 Proline residue: H 96 - end of helix removed outlier: 4.024A pdb=" N TYR H 105 " --> pdb=" O HIS H 101 " (cutoff:3.500A) Processing helix chain 'H' and resid 126 through 158 removed outlier: 4.047A pdb=" N TYR H 130 " --> pdb=" O ASP H 126 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N LYS H 133 " --> pdb=" O SER H 129 " (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: 4.069A 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: 4.014A pdb=" N GLY C 689 " --> pdb=" O THR C 685 " (cutoff:3.500A) Processing helix chain 'C' and resid 706 through 714 Processing helix chain 'C' and resid 741 through 756 removed outlier: 4.171A pdb=" N LEU C 748 " --> pdb=" O ASN C 744 " (cutoff:3.500A) removed outlier: 4.192A 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: 3.582A pdb=" N PHE C 796 " --> pdb=" O VAL C 792 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ALA C 820 " --> pdb=" O TYR C 816 " (cutoff:3.500A) Processing helix chain 'D' and resid 423 through 437 removed outlier: 3.659A 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 487 Processing helix chain 'D' and resid 522 through 546 removed outlier: 3.660A pdb=" N SER D 544 " --> pdb=" O LEU D 540 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ARG D 545 " --> pdb=" O PHE D 541 " (cutoff:3.500A) Processing helix chain 'D' and resid 599 through 627 removed outlier: 3.693A pdb=" N VAL D 626 " --> pdb=" O ALA D 622 " (cutoff:3.500A) Processing helix chain 'D' and resid 635 through 642 removed outlier: 4.090A pdb=" N LEU D 639 " --> pdb=" O SER D 635 " (cutoff:3.500A) Processing helix chain 'D' and resid 653 through 661 removed outlier: 3.527A pdb=" N GLU D 657 " --> pdb=" O GLY D 653 " (cutoff:3.500A) Processing helix chain 'D' and resid 666 through 676 Processing helix chain 'D' and resid 685 through 696 Processing helix chain 'D' and resid 706 through 715 Processing helix chain 'D' and resid 741 through 757 removed outlier: 4.665A pdb=" N ALA D 745 " --> pdb=" O SER D 741 " (cutoff:3.500A) removed outlier: 3.915A 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: 3.660A pdb=" N PHE D 796 " --> pdb=" O VAL D 792 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ARG D 819 " --> pdb=" O CYS D 815 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 395 through 399 removed outlier: 6.200A pdb=" N VAL A 395 " --> pdb=" O LYS A 441 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N THR A 443 " --> pdb=" O VAL A 395 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N VAL A 397 " --> pdb=" O THR A 443 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 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: 3.614A 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: 6.643A pdb=" N ALA A 646 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N LEU A 703 " --> pdb=" O ALA A 646 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N GLY A 648 " --> pdb=" O LEU A 703 " (cutoff:3.500A) removed outlier: 9.133A pdb=" N GLU A 705 " --> pdb=" O GLY A 648 " (cutoff:3.500A) removed outlier: 9.240A pdb=" N TYR A 700 " --> pdb=" O LYS A 505 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N LYS A 505 " --> pdb=" O TYR A 700 " (cutoff:3.500A) removed outlier: 3.513A 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 453 Processing sheet with id=AA8, first strand: chain 'B' and resid 489 through 491 Processing sheet with id=AA9, first strand: chain 'B' and resid 496 through 498 removed outlier: 3.599A pdb=" N MET B 496 " --> pdb=" O TYR B 732 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 702 through 705 removed outlier: 3.698A pdb=" N LEU B 704 " --> pdb=" O SER B 501 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ILE B 502 " --> pdb=" O VAL B 723 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 395 through 399 removed outlier: 6.204A pdb=" N VAL C 395 " --> pdb=" O LYS C 441 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N THR C 443 " --> pdb=" O VAL C 395 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N VAL C 397 " --> pdb=" O THR C 443 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'C' and resid 407 through 408 Processing sheet with id=AB4, first strand: chain 'C' and resid 496 through 498 removed outlier: 3.618A pdb=" N MET C 496 " --> pdb=" O TYR C 732 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 646 through 648 removed outlier: 6.639A pdb=" N ALA C 646 " --> pdb=" O ALA C 701 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N LEU C 703 " --> pdb=" O ALA C 646 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N GLY C 648 " --> pdb=" O LEU C 703 " (cutoff:3.500A) removed outlier: 9.112A pdb=" N GLU C 705 " --> pdb=" O GLY C 648 " (cutoff:3.500A) removed outlier: 9.234A pdb=" N TYR C 700 " --> pdb=" O LYS C 505 " (cutoff:3.500A) removed outlier: 5.251A pdb=" N LYS C 505 " --> pdb=" O TYR C 700 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE C 504 " --> pdb=" O MET C 721 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 396 through 397 Processing sheet with id=AB7, first strand: chain 'D' and resid 407 through 408 Processing sheet with id=AB8, first strand: chain 'D' and resid 451 through 453 Processing sheet with id=AB9, first strand: chain 'D' and resid 489 through 491 Processing sheet with id=AC1, first strand: chain 'D' and resid 496 through 498 removed outlier: 3.599A pdb=" N MET D 496 " --> pdb=" O TYR D 732 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 702 through 705 removed outlier: 3.699A pdb=" N LEU D 704 " --> pdb=" O SER D 501 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ILE D 502 " --> pdb=" O VAL D 723 " (cutoff:3.500A) 954 hydrogen bonds defined for protein. 2802 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.07 Time building geometry restraints manager: 4.17 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: 15418 1.04 - 1.25: 2170 1.25 - 1.45: 5164 1.45 - 1.65: 9106 1.65 - 1.86: 184 Bond restraints: 32042 Sorted by residual: bond pdb=" CAT ZK1 A 901 " pdb=" OAA ZK1 A 901 " ideal model delta sigma weight residual 1.214 1.397 -0.183 2.00e-02 2.50e+03 8.41e+01 bond pdb=" CAT ZK1 C 901 " pdb=" OAA ZK1 C 901 " ideal model delta sigma weight residual 1.214 1.397 -0.183 2.00e-02 2.50e+03 8.40e+01 bond pdb=" CAU ZK1 B 901 " pdb=" OAB ZK1 B 901 " ideal model delta sigma weight residual 1.215 1.397 -0.182 2.00e-02 2.50e+03 8.28e+01 bond pdb=" CAU ZK1 D 901 " pdb=" OAB ZK1 D 901 " ideal model delta sigma weight residual 1.215 1.397 -0.182 2.00e-02 2.50e+03 8.27e+01 bond pdb=" CAU ZK1 C 901 " pdb=" OAB ZK1 C 901 " ideal model delta sigma weight residual 1.215 1.397 -0.182 2.00e-02 2.50e+03 8.24e+01 ... (remaining 32037 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.40: 57479 5.40 - 10.79: 49 10.79 - 16.19: 2 16.19 - 21.59: 0 21.59 - 26.98: 6 Bond angle restraints: 57536 Sorted by residual: angle pdb=" CG2 THR C 784 " pdb=" CB THR C 784 " pdb=" HB THR C 784 " ideal model delta sigma weight residual 108.00 81.02 26.98 3.00e+00 1.11e-01 8.09e+01 angle pdb=" CG2 THR A 784 " pdb=" CB THR A 784 " pdb=" HB THR A 784 " ideal model delta sigma weight residual 108.00 81.07 26.93 3.00e+00 1.11e-01 8.06e+01 angle pdb=" OG1 THR C 784 " pdb=" CB THR C 784 " pdb=" HB THR C 784 " ideal model delta sigma weight residual 109.00 82.73 26.27 3.00e+00 1.11e-01 7.67e+01 angle pdb=" OG1 THR A 784 " pdb=" CB THR A 784 " pdb=" HB THR A 784 " ideal model delta sigma weight residual 109.00 82.76 26.24 3.00e+00 1.11e-01 7.65e+01 angle pdb=" CA THR A 784 " pdb=" CB THR A 784 " pdb=" HB THR A 784 " ideal model delta sigma weight residual 109.00 83.45 25.55 3.00e+00 1.11e-01 7.25e+01 ... (remaining 57531 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.45: 14999 32.45 - 64.89: 458 64.89 - 97.34: 10 97.34 - 129.78: 11 129.78 - 162.23: 1 Dihedral angle restraints: 15479 sinusoidal: 8106 harmonic: 7373 Sorted by residual: dihedral pdb=" C21 OLC B 902 " pdb=" C1 OLC B 902 " pdb=" O20 OLC B 902 " pdb=" O19 OLC B 902 " ideal model delta sinusoidal sigma weight residual -1.92 160.31 -162.23 1 3.00e+01 1.11e-03 2.08e+01 dihedral pdb=" NAX ZK1 D 901 " pdb=" CAK ZK1 D 901 " pdb=" CAM ZK1 D 901 " pdb=" OAQ ZK1 D 901 " ideal model delta sinusoidal sigma weight residual -57.16 64.38 -121.54 1 3.00e+01 1.11e-03 1.62e+01 dihedral pdb=" O20 OLC B 902 " pdb=" C21 OLC B 902 " pdb=" C22 OLC B 902 " pdb=" O23 OLC B 902 " ideal model delta sinusoidal sigma weight residual -57.23 -175.56 118.33 1 3.00e+01 1.11e-03 1.57e+01 ... (remaining 15476 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.276: 2536 0.276 - 0.552: 4 0.552 - 0.828: 0 0.828 - 1.103: 0 1.103 - 1.379: 2 Chirality restraints: 2542 Sorted by residual: chirality pdb=" CB THR A 784 " pdb=" CA THR A 784 " pdb=" OG1 THR A 784 " pdb=" CG2 THR A 784 " both_signs ideal model delta sigma weight residual False 2.55 1.17 1.38 2.00e-01 2.50e+01 4.76e+01 chirality pdb=" CB THR C 784 " pdb=" CA THR C 784 " pdb=" OG1 THR C 784 " pdb=" CG2 THR C 784 " both_signs ideal model delta sigma weight residual False 2.55 1.17 1.38 2.00e-01 2.50e+01 4.74e+01 chirality pdb=" C22 OLC D 902 " pdb=" C21 OLC D 902 " pdb=" C24 OLC D 902 " pdb=" O23 OLC D 902 " both_signs ideal model delta sigma weight residual False -2.31 -2.80 0.49 2.00e-01 2.50e+01 6.03e+00 ... (remaining 2539 not shown) Planarity restraints: 4654 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C10 OLC D 902 " -0.341 2.00e-02 2.50e+03 2.46e-01 6.05e+02 pdb=" C11 OLC D 902 " 0.113 2.00e-02 2.50e+03 pdb=" C8 OLC D 902 " -0.094 2.00e-02 2.50e+03 pdb=" C9 OLC D 902 " 0.322 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 OLC A 902 " -0.323 2.00e-02 2.50e+03 2.41e-01 5.82e+02 pdb=" C11 OLC A 902 " 0.100 2.00e-02 2.50e+03 pdb=" C8 OLC A 902 " -0.105 2.00e-02 2.50e+03 pdb=" C9 OLC A 902 " 0.328 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 OLC B 902 " 0.181 2.00e-02 2.50e+03 1.96e-01 3.85e+02 pdb=" C11 OLC B 902 " -0.192 2.00e-02 2.50e+03 pdb=" C8 OLC B 902 " -0.200 2.00e-02 2.50e+03 pdb=" C9 OLC B 902 " 0.211 2.00e-02 2.50e+03 ... (remaining 4651 not shown) Histogram of nonbonded interaction distances: 1.53 - 2.15: 1051 2.15 - 2.76: 59557 2.76 - 3.37: 88410 3.37 - 3.99: 109012 3.99 - 4.60: 173445 Nonbonded interactions: 431475 Sorted by model distance: nonbonded pdb="HH22 ARG B 545 " pdb=" O LYS G 66 " model vdw 1.534 2.450 nonbonded pdb="HH12 ARG B 485 " pdb=" OAA ZK1 B 901 " model vdw 1.556 2.450 nonbonded pdb=" HZ1 LYS D 505 " pdb=" O ARG D 694 " model vdw 1.587 2.450 nonbonded pdb=" HZ1 LYS B 505 " pdb=" O ARG B 694 " model vdw 1.588 2.450 nonbonded pdb=" H ILE C 500 " pdb=" OD1 ASP C 728 " model vdw 1.594 2.450 ... (remaining 431470 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 394 through 598 or (resid 599 and (name N or name CA or na \ me C or name O or name CB or name CG or name CD or name NE or name CZ or name NH \ 1 or name NH2)) or resid 600 through 674 or (resid 675 and (name N or name CA or \ name C or name O or name CB or name H or name HA )) or resid 676 through 704 or \ (resid 705 and (name N or name CA or name C or name O or name CB or name H or n \ ame HA )) or resid 706 through 776 or (resid 784 and (name N or name CA or name \ C or name O or name CB or name HA )) or (resid 785 and (name N or name CA or nam \ e C or name O or name CB or name H or name HA )) or resid 786 through 902)) selection = (chain 'B' and ((resid 394 and (name CA or name C or name O or name CB or name O \ G1 or name CG2 or name HB or name HG1 or name HG21 or name HG22 or name HG23)) o \ r (resid 395 and (name N or name CA or name C or name O or name CB or name H or \ name HA )) or resid 396 through 417 or (resid 418 through 419 and (name N or nam \ e CA or name C or name O or name CB or name H or name HA )) or resid 420 through \ 421 or (resid 422 and (name N or name CA or name C or name O or name CB or name \ H or name HA )) or resid 423 through 433 or (resid 434 and (name N or name CA o \ r name C or name O or name CB or name H or name HA )) or resid 435 through 505 o \ r (resid 506 and (name N or name CA or name C or name O or name CB or name H or \ name HA )) or resid 507 through 539 or (resid 540 and (name N or name CA or name \ C or name O or name CB or name H or name HA )) or resid 541 through 637 or (res \ id 638 and (name N or name CA or name C or name O or name CB or name H or name H \ A )) or resid 639 through 660 or (resid 661 and (name N or name CA or name C or \ name O or name CB or name H or name HA )) or resid 662 through 822 or (resid 823 \ through 824 and (name N or name CA or name C or name O or name CB or name H or \ name HA )) or resid 901 through 902)) selection = (chain 'C' and (resid 394 through 598 or (resid 599 and (name N or name CA or na \ me C or name O or name CB or name CG or name CD or name NE or name CZ or name NH \ 1 or name NH2)) or resid 600 through 660 or (resid 661 and (name N or name CA or \ name C or name O or name CB or name H or name HA )) or resid 662 through 674 or \ (resid 675 and (name N or name CA or name C or name O or name CB or name H or n \ ame HA )) or resid 676 through 704 or (resid 705 and (name N or name CA or name \ C or name O or name CB or name H or name HA )) or resid 706 through 776 or (resi \ d 784 and (name N or name CA or name C or name O or name CB or name HA )) or (re \ sid 785 and (name N or name CA or name C or name O or name CB or name H or name \ HA )) or resid 786 through 902)) selection = (chain 'D' and ((resid 394 and (name CA or name C or name O or name CB or name O \ G1 or name CG2 or name HB or name HG1 or name HG21 or name HG22 or name HG23)) o \ r (resid 395 and (name N or name CA or name C or name O or name CB or name H or \ name HA )) or resid 396 through 417 or (resid 418 through 419 and (name N or nam \ e CA or name C or name O or name CB or name H or name HA )) or resid 420 through \ 421 or (resid 422 and (name N or name CA or name C or name O or name CB or name \ H or name HA )) or resid 423 through 433 or (resid 434 and (name N or name CA o \ r name C or name O or name CB or name H or name HA )) or resid 435 through 505 o \ r (resid 506 and (name N or name CA or name C or name O or name CB or name H or \ name HA )) or resid 507 through 539 or (resid 540 and (name N or name CA or name \ C or name O or name CB or name H or name HA )) or resid 541 through 637 or (res \ id 638 and (name N or name CA or name C or name O or name CB or name H or name H \ A )) or resid 639 through 660 or (resid 661 and (name N or name CA or name C or \ name O or name CB or name H or name HA )) or resid 662 through 822 or (resid 823 \ through 824 and (name N or name CA or name C or name O or name CB or name H or \ name HA )) or resid 901 through 902)) } ncs_group { reference = (chain 'E' and (resid 2 through 108 or (resid 110 and (name N or name CA or name \ C or name O or name CB )) or (resid 126 and (name N or name CA or name C or nam \ e O or name CB or name CG or name OD1 or name OD2)) or (resid 127 and (name N or \ name CA or name C or name O or name CB or name OG1 or name CG2 or name HA )) or \ (resid 128 and (name N or name CA or name C or name O or name CB or name CG or \ name CD1 or name CD2 or name H or name HA )) or resid 129 through 159)) selection = (chain 'F' and (resid 2 through 30 or (resid 31 and (name N or name CA or name C \ or name O or name CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 \ or name CZ )) or resid 32 through 37 or (resid 50 and (name N or name CA or nam \ e C or name O or name CB or name HA or name HB1 or name HB2 or name HB3)) or (re \ sid 51 through 58 and (name N or name CA or name C or name O or name CB or name \ H or name HA )) or resid 59 through 86 or (resid 87 and (name N or name CA or na \ me C or name O or name CB or name CG or name CD or name OE1 or name OE2 or name \ H or name HA )) or resid 88 through 108 or resid 125 through 159)) selection = (chain 'G' and (resid 2 through 30 or (resid 31 and (name N or name CA or name C \ or name O or name CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 \ or name CZ )) or resid 32 through 108 or (resid 110 and (name N or name CA or n \ ame C or name O or name CB )) or (resid 126 and (name N or name CA or name C or \ name O or name CB or name CG or name OD1 or name OD2)) or (resid 127 and (name N \ or name CA or name C or name O or name CB or name OG1 or name CG2 or name HA )) \ or (resid 128 and (name N or name CA or name C or name O or name CB or name CG \ or name CD1 or name CD2 or name H or name HA )) or resid 129 through 159)) selection = (chain 'H' and (resid 2 through 30 or (resid 31 and (name N or name CA or name C \ or name O or name CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 \ or name CZ )) or resid 32 through 37 or (resid 50 and (name N or name CA or nam \ e C or name O or name CB or name HA or name HB1 or name HB2 or name HB3)) or (re \ sid 51 through 58 and (name N or name CA or name C or name O or name CB or name \ H or name HA )) or resid 59 through 86 or (resid 87 and (name N or name CA or na \ me C or name O or name CB or name CG or name CD or name OE1 or name OE2 or name \ H or name HA )) or resid 88 through 108 or resid 125 through 159)) } 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: 4.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.180 Extract box with map and model: 0.490 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 29.850 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7344 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 16576 Z= 0.383 Angle : 0.629 11.312 22491 Z= 0.298 Chirality : 0.057 1.379 2542 Planarity : 0.008 0.246 2697 Dihedral : 14.044 162.228 6029 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 0.12 % Allowed : 2.08 % Favored : 97.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.11 (0.16), residues: 1996 helix: -0.98 (0.13), residues: 1226 sheet: -3.01 (0.42), residues: 120 loop : -3.92 (0.18), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 59 TYR 0.013 0.001 TYR H 155 PHE 0.012 0.001 PHE H 22 TRP 0.008 0.001 TRP B 606 HIS 0.003 0.001 HIS E 75 Details of bonding type rmsd covalent geometry : bond 0.00785 (16572) covalent geometry : angle 0.62882 (22483) SS BOND : bond 0.00310 ( 4) SS BOND : angle 0.52772 ( 8) hydrogen bonds : bond 0.12413 ( 954) hydrogen bonds : angle 5.45166 ( 2802) *********************** 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 VAL 395 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 434 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 506 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 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 697 is missing expected H atoms. Skipping. Residue LYS 699 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 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 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 VAL 395 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 434 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 506 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 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 697 is missing expected H atoms. Skipping. Residue LYS 699 is missing expected H atoms. Skipping. Residue THR 784 is missing expected H atoms. Skipping. Residue SER 785 is missing expected H atoms. Skipping. Evaluate side-chains 311 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 309 time to evaluate : 0.798 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 764 ASN cc_start: 0.7915 (m-40) cc_final: 0.7606 (m110) REVERT: B 760 ASP cc_start: 0.8275 (p0) cc_final: 0.8056 (p0) REVERT: E 88 TRP cc_start: 0.5486 (m100) cc_final: 0.5023 (m100) REVERT: E 147 PHE cc_start: 0.7126 (m-10) cc_final: 0.6662 (t80) REVERT: F 22 PHE cc_start: 0.5900 (OUTLIER) cc_final: 0.5603 (t80) REVERT: F 66 LYS cc_start: 0.6676 (mtpt) cc_final: 0.6237 (mmtp) REVERT: G 33 GLU cc_start: 0.6167 (tt0) cc_final: 0.5579 (tm-30) REVERT: G 88 TRP cc_start: 0.5567 (m100) cc_final: 0.5070 (m100) REVERT: G 147 PHE cc_start: 0.7460 (m-10) cc_final: 0.6774 (t80) REVERT: H 22 PHE cc_start: 0.5979 (OUTLIER) cc_final: 0.5156 (t80) REVERT: H 66 LYS cc_start: 0.7128 (mtpt) cc_final: 0.6540 (mmtp) REVERT: C 764 ASN cc_start: 0.8006 (m-40) cc_final: 0.7757 (m110) REVERT: D 412 HIS cc_start: 0.6977 (p90) cc_final: 0.6738 (p-80) REVERT: D 596 LEU cc_start: 0.8690 (tp) cc_final: 0.8358 (tp) outliers start: 2 outliers final: 0 residues processed: 311 average time/residue: 0.2929 time to fit residues: 131.5720 Evaluate side-chains 185 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 183 time to evaluate : 0.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 22 PHE Chi-restraints excluded: chain H residue 22 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 2.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 9.9990 chunk 77 optimal weight: 7.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 8.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 791 ASN E 132 GLN F 94 ASN F 132 GLN H 94 ASN C 791 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.118812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.099019 restraints weight = 124602.536| |-----------------------------------------------------------------------------| r_work (start): 0.3604 rms_B_bonded: 3.23 r_work: 0.3488 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.2482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.096 16576 Z= 0.219 Angle : 0.590 11.189 22491 Z= 0.320 Chirality : 0.055 1.392 2542 Planarity : 0.005 0.102 2697 Dihedral : 9.980 163.617 2639 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.21 % Favored : 93.74 % Rotamer: Outliers : 0.80 % Allowed : 8.08 % Favored : 91.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.48 (0.18), residues: 1996 helix: 0.23 (0.14), residues: 1238 sheet: -2.37 (0.48), residues: 110 loop : -3.11 (0.22), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG B 661 TYR 0.018 0.001 TYR F 155 PHE 0.019 0.001 PHE E 23 TRP 0.008 0.001 TRP B 606 HIS 0.008 0.001 HIS E 107 Details of bonding type rmsd covalent geometry : bond 0.00486 (16572) covalent geometry : angle 0.59007 (22483) SS BOND : bond 0.00530 ( 4) SS BOND : angle 0.82110 ( 8) hydrogen bonds : bond 0.03859 ( 954) hydrogen bonds : angle 4.52096 ( 2802) *********************** 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 VAL 395 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 434 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 506 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 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 697 is missing expected H atoms. Skipping. Residue LYS 699 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 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 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 VAL 395 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 434 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 506 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 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 697 is missing expected H atoms. Skipping. Residue LYS 699 is missing expected H atoms. Skipping. Residue THR 784 is missing expected H atoms. Skipping. Residue SER 785 is missing expected H atoms. Skipping. Evaluate side-chains 216 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 203 time to evaluate : 0.934 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 599 ARG cc_start: 0.8534 (mtt-85) cc_final: 0.7701 (mmt180) REVERT: B 760 ASP cc_start: 0.8721 (p0) cc_final: 0.8499 (p0) REVERT: E 147 PHE cc_start: 0.7393 (m-10) cc_final: 0.6756 (t80) REVERT: F 22 PHE cc_start: 0.5890 (OUTLIER) cc_final: 0.5525 (t80) REVERT: F 66 LYS cc_start: 0.6505 (mtpt) cc_final: 0.6142 (mmtp) REVERT: G 33 GLU cc_start: 0.6450 (tt0) cc_final: 0.5757 (tm-30) REVERT: G 147 PHE cc_start: 0.7707 (m-10) cc_final: 0.6915 (t80) REVERT: H 22 PHE cc_start: 0.5646 (OUTLIER) cc_final: 0.5111 (t80) REVERT: H 66 LYS cc_start: 0.6943 (mtpt) cc_final: 0.6318 (mmtp) REVERT: C 463 MET cc_start: 0.8541 (mtm) cc_final: 0.8146 (mtm) REVERT: D 596 LEU cc_start: 0.9104 (tp) cc_final: 0.8878 (tp) REVERT: D 726 ASN cc_start: 0.8351 (m-40) cc_final: 0.7838 (m-40) outliers start: 13 outliers final: 6 residues processed: 213 average time/residue: 0.2644 time to fit residues: 86.9468 Evaluate side-chains 186 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 178 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 631 SER Chi-restraints excluded: chain B residue 613 ILE Chi-restraints excluded: chain E residue 152 CYS Chi-restraints excluded: chain F residue 22 PHE Chi-restraints excluded: chain H residue 22 PHE Chi-restraints excluded: chain C residue 789 LEU Chi-restraints excluded: chain D residue 649 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 154 optimal weight: 1.9990 chunk 147 optimal weight: 1.9990 chunk 180 optimal weight: 0.6980 chunk 65 optimal weight: 0.5980 chunk 166 optimal weight: 5.9990 chunk 22 optimal weight: 3.9990 chunk 136 optimal weight: 0.6980 chunk 194 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 48 optimal weight: 0.6980 chunk 190 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 94 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.120374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.100656 restraints weight = 123116.190| |-----------------------------------------------------------------------------| r_work (start): 0.3630 rms_B_bonded: 3.24 r_work: 0.3514 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.2831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 16576 Z= 0.107 Angle : 0.479 11.171 22491 Z= 0.256 Chirality : 0.053 1.382 2542 Planarity : 0.003 0.044 2697 Dihedral : 8.863 101.399 2639 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 0.92 % Allowed : 8.63 % Favored : 90.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.50 (0.19), residues: 1996 helix: 1.03 (0.15), residues: 1236 sheet: -2.08 (0.46), residues: 124 loop : -2.78 (0.23), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 661 TYR 0.020 0.001 TYR H 155 PHE 0.017 0.001 PHE F 62 TRP 0.005 0.001 TRP B 606 HIS 0.004 0.001 HIS H 75 Details of bonding type rmsd covalent geometry : bond 0.00236 (16572) covalent geometry : angle 0.47919 (22483) SS BOND : bond 0.00289 ( 4) SS BOND : angle 0.48768 ( 8) hydrogen bonds : bond 0.03399 ( 954) hydrogen bonds : angle 4.09221 ( 2802) *********************** 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 VAL 395 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 434 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 506 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 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 697 is missing expected H atoms. Skipping. Residue LYS 699 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 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 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 VAL 395 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 434 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 506 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 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 697 is missing expected H atoms. Skipping. Residue LYS 699 is missing expected H atoms. Skipping. Residue THR 784 is missing expected H atoms. Skipping. Residue SER 785 is missing expected H atoms. Skipping. Evaluate side-chains 206 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 191 time to evaluate : 0.892 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 599 ARG cc_start: 0.8492 (mtt-85) cc_final: 0.7627 (mmt180) REVERT: E 82 PHE cc_start: 0.7258 (m-10) cc_final: 0.6944 (m-10) REVERT: E 88 TRP cc_start: 0.5875 (m100) cc_final: 0.5307 (m100) REVERT: E 147 PHE cc_start: 0.7343 (m-10) cc_final: 0.6702 (t80) REVERT: F 12 LEU cc_start: 0.8343 (OUTLIER) cc_final: 0.8124 (mp) REVERT: F 22 PHE cc_start: 0.5880 (OUTLIER) cc_final: 0.5386 (t80) REVERT: F 66 LYS cc_start: 0.6507 (mtpt) cc_final: 0.6186 (mmtp) REVERT: G 33 GLU cc_start: 0.6447 (tt0) cc_final: 0.5732 (tm-30) REVERT: G 146 PHE cc_start: 0.6797 (t80) cc_final: 0.6584 (t80) REVERT: G 147 PHE cc_start: 0.7669 (m-10) cc_final: 0.6887 (t80) REVERT: H 66 LYS cc_start: 0.6853 (mtpt) cc_final: 0.6322 (mmtp) REVERT: C 408 MET cc_start: 0.7024 (mmm) cc_final: 0.6554 (mmm) REVERT: D 596 LEU cc_start: 0.9096 (tp) cc_final: 0.8883 (tp) REVERT: D 726 ASN cc_start: 0.8339 (m-40) cc_final: 0.7783 (m-40) outliers start: 15 outliers final: 6 residues processed: 204 average time/residue: 0.2702 time to fit residues: 84.5987 Evaluate side-chains 184 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 176 time to evaluate : 0.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 631 SER Chi-restraints excluded: chain A residue 789 LEU Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 22 PHE Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain C residue 789 LEU Chi-restraints excluded: chain D residue 649 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 198 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 85 optimal weight: 5.9990 chunk 143 optimal weight: 0.9980 chunk 34 optimal weight: 0.6980 chunk 48 optimal weight: 0.9980 chunk 6 optimal weight: 4.9990 chunk 163 optimal weight: 2.9990 chunk 83 optimal weight: 0.8980 chunk 184 optimal weight: 2.9990 chunk 188 optimal weight: 3.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.118675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.098967 restraints weight = 122422.804| |-----------------------------------------------------------------------------| r_work (start): 0.3597 rms_B_bonded: 3.17 r_work: 0.3480 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.3239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 16576 Z= 0.139 Angle : 0.489 11.174 22491 Z= 0.264 Chirality : 0.053 1.380 2542 Planarity : 0.004 0.042 2697 Dihedral : 8.738 102.499 2637 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.41 % Favored : 94.54 % Rotamer: Outliers : 0.92 % Allowed : 10.04 % Favored : 89.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.19), residues: 1996 helix: 1.33 (0.15), residues: 1236 sheet: -1.94 (0.47), residues: 124 loop : -2.57 (0.24), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 104 TYR 0.024 0.001 TYR F 148 PHE 0.013 0.001 PHE E 23 TRP 0.006 0.001 TRP B 766 HIS 0.004 0.001 HIS H 75 Details of bonding type rmsd covalent geometry : bond 0.00309 (16572) covalent geometry : angle 0.48911 (22483) SS BOND : bond 0.00351 ( 4) SS BOND : angle 0.59314 ( 8) hydrogen bonds : bond 0.03268 ( 954) hydrogen bonds : angle 3.99346 ( 2802) *********************** 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 VAL 395 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 434 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 506 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 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 697 is missing expected H atoms. Skipping. Residue LYS 699 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 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 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 VAL 395 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 434 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 506 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 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 697 is missing expected H atoms. Skipping. Residue LYS 699 is missing expected H atoms. Skipping. Residue THR 784 is missing expected H atoms. Skipping. Residue SER 785 is missing expected H atoms. Skipping. Evaluate side-chains 208 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 193 time to evaluate : 0.856 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 599 ARG cc_start: 0.8529 (mtt-85) cc_final: 0.7662 (mmt180) REVERT: E 80 ILE cc_start: 0.9121 (mm) cc_final: 0.8905 (mt) REVERT: E 88 TRP cc_start: 0.6003 (m100) cc_final: 0.5483 (m100) REVERT: E 147 PHE cc_start: 0.7361 (m-10) cc_final: 0.6750 (t80) REVERT: F 12 LEU cc_start: 0.8379 (OUTLIER) cc_final: 0.8005 (mp) REVERT: F 22 PHE cc_start: 0.5917 (OUTLIER) cc_final: 0.5424 (t80) REVERT: F 66 LYS cc_start: 0.6588 (mtpt) cc_final: 0.6256 (mmtp) REVERT: G 33 GLU cc_start: 0.6612 (tt0) cc_final: 0.5862 (tm-30) REVERT: G 147 PHE cc_start: 0.7686 (m-10) cc_final: 0.6883 (t80) REVERT: H 66 LYS cc_start: 0.6797 (mtpt) cc_final: 0.6255 (mmtp) REVERT: C 599 ARG cc_start: 0.8586 (mtt-85) cc_final: 0.7697 (mmt180) REVERT: D 726 ASN cc_start: 0.8335 (m-40) cc_final: 0.7803 (m-40) outliers start: 15 outliers final: 9 residues processed: 205 average time/residue: 0.2639 time to fit residues: 84.2702 Evaluate side-chains 194 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 183 time to evaluate : 0.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 789 LEU Chi-restraints excluded: chain B residue 613 ILE Chi-restraints excluded: chain E residue 27 HIS Chi-restraints excluded: chain E residue 132 GLN Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 22 PHE Chi-restraints excluded: chain C residue 502 ILE Chi-restraints excluded: chain C residue 773 CYS Chi-restraints excluded: chain C residue 789 LEU Chi-restraints excluded: chain D residue 649 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 17 optimal weight: 1.9990 chunk 188 optimal weight: 3.9990 chunk 114 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 142 optimal weight: 2.9990 chunk 129 optimal weight: 3.9990 chunk 86 optimal weight: 5.9990 chunk 113 optimal weight: 2.9990 chunk 42 optimal weight: 4.9990 chunk 131 optimal weight: 3.9990 chunk 162 optimal weight: 3.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- 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 = 0.3873 r_free = 0.3873 target = 0.114458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.093980 restraints weight = 126433.621| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 3.26 r_work: 0.3385 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.3939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 16576 Z= 0.256 Angle : 0.596 11.198 22491 Z= 0.325 Chirality : 0.055 1.382 2542 Planarity : 0.004 0.043 2697 Dihedral : 9.296 105.220 2637 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.16 % Favored : 92.79 % Rotamer: Outliers : 1.53 % Allowed : 11.82 % Favored : 86.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.19), residues: 1996 helix: 0.94 (0.14), residues: 1254 sheet: -1.78 (0.48), residues: 116 loop : -2.58 (0.24), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 628 TYR 0.019 0.002 TYR H 155 PHE 0.015 0.002 PHE H 106 TRP 0.007 0.001 TRP D 460 HIS 0.004 0.001 HIS E 75 Details of bonding type rmsd covalent geometry : bond 0.00566 (16572) covalent geometry : angle 0.59549 (22483) SS BOND : bond 0.00676 ( 4) SS BOND : angle 0.91081 ( 8) hydrogen bonds : bond 0.03909 ( 954) hydrogen bonds : angle 4.31293 ( 2802) *********************** 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 VAL 395 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 434 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 506 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 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 697 is missing expected H atoms. Skipping. Residue LYS 699 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 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 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 VAL 395 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 434 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 506 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 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 697 is missing expected H atoms. Skipping. Residue LYS 699 is missing expected H atoms. Skipping. Residue THR 784 is missing expected H atoms. Skipping. Residue SER 785 is missing expected H atoms. Skipping. Evaluate side-chains 219 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 194 time to evaluate : 0.738 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 599 ARG cc_start: 0.8795 (mtt-85) cc_final: 0.7869 (mmp80) REVERT: B 629 MET cc_start: 0.8589 (mtt) cc_final: 0.8111 (mtt) REVERT: E 80 ILE cc_start: 0.9259 (mm) cc_final: 0.9008 (mt) REVERT: E 147 PHE cc_start: 0.7702 (m-10) cc_final: 0.6848 (t80) REVERT: F 22 PHE cc_start: 0.5891 (OUTLIER) cc_final: 0.5339 (t80) REVERT: F 66 LYS cc_start: 0.6504 (mtpt) cc_final: 0.6175 (mmtp) REVERT: G 33 GLU cc_start: 0.6744 (tt0) cc_final: 0.5797 (tm-30) REVERT: H 66 LYS cc_start: 0.6898 (mtpt) cc_final: 0.6319 (mmtp) REVERT: C 599 ARG cc_start: 0.8849 (mtt-85) cc_final: 0.7900 (mmp80) REVERT: D 629 MET cc_start: 0.8508 (mtt) cc_final: 0.8071 (mtt) outliers start: 25 outliers final: 19 residues processed: 210 average time/residue: 0.2480 time to fit residues: 82.3814 Evaluate side-chains 199 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 179 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 773 CYS Chi-restraints excluded: chain A residue 789 LEU Chi-restraints excluded: chain A residue 798 ILE Chi-restraints excluded: chain B residue 683 VAL Chi-restraints excluded: chain E residue 27 HIS Chi-restraints excluded: chain E residue 132 GLN Chi-restraints excluded: chain F residue 22 PHE Chi-restraints excluded: chain G residue 75 HIS Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain C residue 502 ILE Chi-restraints excluded: chain C residue 538 VAL Chi-restraints excluded: chain C residue 773 CYS Chi-restraints excluded: chain C residue 789 LEU Chi-restraints excluded: chain D residue 649 THR Chi-restraints excluded: chain D residue 683 VAL Chi-restraints excluded: chain D residue 807 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 13 optimal weight: 0.7980 chunk 155 optimal weight: 2.9990 chunk 171 optimal weight: 0.6980 chunk 63 optimal weight: 3.9990 chunk 99 optimal weight: 2.9990 chunk 6 optimal weight: 0.0980 chunk 58 optimal weight: 1.9990 chunk 50 optimal weight: 0.6980 chunk 114 optimal weight: 3.9990 chunk 133 optimal weight: 1.9990 chunk 76 optimal weight: 7.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 = 0.3916 r_free = 0.3916 target = 0.117828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.097162 restraints weight = 121996.493| |-----------------------------------------------------------------------------| r_work (start): 0.3559 rms_B_bonded: 3.30 r_work: 0.3439 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.4142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16576 Z= 0.113 Angle : 0.493 11.196 22491 Z= 0.264 Chirality : 0.053 1.377 2542 Planarity : 0.003 0.041 2697 Dihedral : 8.547 98.512 2637 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 1.29 % Allowed : 12.98 % Favored : 85.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.19), residues: 1996 helix: 1.40 (0.15), residues: 1254 sheet: -1.67 (0.47), residues: 124 loop : -2.44 (0.25), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 628 TYR 0.019 0.001 TYR H 155 PHE 0.013 0.001 PHE E 23 TRP 0.006 0.001 TRP B 605 HIS 0.003 0.001 HIS G 27 Details of bonding type rmsd covalent geometry : bond 0.00253 (16572) covalent geometry : angle 0.49276 (22483) SS BOND : bond 0.00278 ( 4) SS BOND : angle 0.58836 ( 8) hydrogen bonds : bond 0.03278 ( 954) hydrogen bonds : angle 3.92813 ( 2802) *********************** 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 VAL 395 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 434 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 506 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 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 697 is missing expected H atoms. Skipping. Residue LYS 699 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 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 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 VAL 395 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 434 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 506 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 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 697 is missing expected H atoms. Skipping. Residue LYS 699 is missing expected H atoms. Skipping. Residue THR 784 is missing expected H atoms. Skipping. Residue SER 785 is missing expected H atoms. Skipping. Evaluate side-chains 209 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 188 time to evaluate : 0.808 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 599 ARG cc_start: 0.8771 (mtt-85) cc_final: 0.7820 (mmp80) REVERT: E 80 ILE cc_start: 0.9252 (mm) cc_final: 0.9025 (mt) REVERT: E 87 GLU cc_start: 0.7825 (mm-30) cc_final: 0.7599 (mm-30) REVERT: E 147 PHE cc_start: 0.7654 (m-10) cc_final: 0.6807 (t80) REVERT: F 22 PHE cc_start: 0.5950 (OUTLIER) cc_final: 0.5369 (t80) REVERT: F 66 LYS cc_start: 0.6456 (mtpt) cc_final: 0.6156 (mmtp) REVERT: G 33 GLU cc_start: 0.6742 (tt0) cc_final: 0.5811 (tm-30) REVERT: G 146 PHE cc_start: 0.6724 (t80) cc_final: 0.6510 (t80) REVERT: G 147 PHE cc_start: 0.7741 (m-10) cc_final: 0.6806 (t80) REVERT: H 66 LYS cc_start: 0.6882 (mtpt) cc_final: 0.6300 (mmtp) REVERT: C 599 ARG cc_start: 0.8799 (mtt-85) cc_final: 0.7832 (mmp80) outliers start: 21 outliers final: 18 residues processed: 204 average time/residue: 0.2493 time to fit residues: 80.0532 Evaluate side-chains 198 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 179 time to evaluate : 0.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 613 ILE Chi-restraints excluded: chain A residue 773 CYS Chi-restraints excluded: chain A residue 789 LEU Chi-restraints excluded: chain E residue 27 HIS Chi-restraints excluded: chain E residue 132 GLN Chi-restraints excluded: chain F residue 22 PHE Chi-restraints excluded: chain G residue 23 PHE Chi-restraints excluded: chain G residue 75 HIS Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain H residue 88 TRP Chi-restraints excluded: chain C residue 502 ILE Chi-restraints excluded: chain C residue 538 VAL Chi-restraints excluded: chain C residue 708 MET Chi-restraints excluded: chain C residue 773 CYS Chi-restraints excluded: chain C residue 789 LEU Chi-restraints excluded: chain D residue 649 THR Chi-restraints excluded: chain D residue 807 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 154 optimal weight: 3.9990 chunk 105 optimal weight: 5.9990 chunk 169 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 chunk 54 optimal weight: 0.3980 chunk 98 optimal weight: 1.9990 chunk 188 optimal weight: 4.9990 chunk 4 optimal weight: 5.9990 chunk 66 optimal weight: 0.9990 chunk 10 optimal weight: 0.1980 chunk 24 optimal weight: 3.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- 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 = 0.3903 r_free = 0.3903 target = 0.117086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.096498 restraints weight = 123046.162| |-----------------------------------------------------------------------------| r_work (start): 0.3547 rms_B_bonded: 3.23 r_work: 0.3428 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.4288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16576 Z= 0.152 Angle : 0.505 11.179 22491 Z= 0.272 Chirality : 0.053 1.374 2542 Planarity : 0.003 0.042 2697 Dihedral : 8.542 103.192 2637 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 1.29 % Allowed : 13.66 % Favored : 85.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.19), residues: 1996 helix: 1.48 (0.15), residues: 1256 sheet: -1.61 (0.47), residues: 124 loop : -2.40 (0.25), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 485 TYR 0.009 0.001 TYR F 130 PHE 0.013 0.001 PHE E 23 TRP 0.006 0.001 TRP H 103 HIS 0.003 0.001 HIS E 75 Details of bonding type rmsd covalent geometry : bond 0.00339 (16572) covalent geometry : angle 0.50468 (22483) SS BOND : bond 0.00423 ( 4) SS BOND : angle 0.56772 ( 8) hydrogen bonds : bond 0.03320 ( 954) hydrogen bonds : angle 3.95011 ( 2802) *********************** 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 VAL 395 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 434 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 506 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 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 697 is missing expected H atoms. Skipping. Residue LYS 699 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 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 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 VAL 395 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 434 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 506 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 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 697 is missing expected H atoms. Skipping. Residue LYS 699 is missing expected H atoms. Skipping. Residue THR 784 is missing expected H atoms. Skipping. Residue SER 785 is missing expected H atoms. Skipping. Evaluate side-chains 203 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 182 time to evaluate : 0.934 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 599 ARG cc_start: 0.8794 (mtt-85) cc_final: 0.7835 (mmp80) REVERT: E 80 ILE cc_start: 0.9243 (mm) cc_final: 0.8994 (mt) REVERT: E 87 GLU cc_start: 0.7966 (mm-30) cc_final: 0.7742 (mm-30) REVERT: E 147 PHE cc_start: 0.7648 (m-10) cc_final: 0.6781 (t80) REVERT: F 66 LYS cc_start: 0.6455 (mtpt) cc_final: 0.6086 (mmtp) REVERT: G 33 GLU cc_start: 0.6810 (tt0) cc_final: 0.5862 (tm-30) REVERT: G 146 PHE cc_start: 0.6730 (t80) cc_final: 0.6514 (t80) REVERT: G 147 PHE cc_start: 0.7755 (m-10) cc_final: 0.6816 (t80) REVERT: H 66 LYS cc_start: 0.6704 (mtpt) cc_final: 0.6222 (mmtp) REVERT: C 599 ARG cc_start: 0.8787 (mtt-85) cc_final: 0.7803 (mmp80) REVERT: C 656 LYS cc_start: 0.8957 (OUTLIER) cc_final: 0.8527 (ptpp) outliers start: 21 outliers final: 19 residues processed: 198 average time/residue: 0.2599 time to fit residues: 80.6538 Evaluate side-chains 200 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 180 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 773 CYS Chi-restraints excluded: chain A residue 789 LEU Chi-restraints excluded: chain E residue 27 HIS Chi-restraints excluded: chain E residue 75 HIS Chi-restraints excluded: chain E residue 132 GLN Chi-restraints excluded: chain G residue 23 PHE Chi-restraints excluded: chain G residue 75 HIS Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain C residue 502 ILE Chi-restraints excluded: chain C residue 656 LYS Chi-restraints excluded: chain C residue 708 MET Chi-restraints excluded: chain C residue 773 CYS Chi-restraints excluded: chain C residue 789 LEU Chi-restraints excluded: chain D residue 649 THR Chi-restraints excluded: chain D residue 807 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 92 optimal weight: 2.9990 chunk 116 optimal weight: 6.9990 chunk 36 optimal weight: 2.9990 chunk 75 optimal weight: 0.7980 chunk 4 optimal weight: 5.9990 chunk 186 optimal weight: 0.8980 chunk 155 optimal weight: 2.9990 chunk 147 optimal weight: 5.9990 chunk 65 optimal weight: 4.9990 chunk 100 optimal weight: 3.9990 chunk 131 optimal weight: 0.0040 overall best weight: 1.5396 ------------------------------------------------------------------------------- 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 = 0.3894 r_free = 0.3894 target = 0.117116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.096333 restraints weight = 124179.921| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 3.31 r_work: 0.3417 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.4474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16576 Z= 0.149 Angle : 0.501 11.196 22491 Z= 0.270 Chirality : 0.053 1.375 2542 Planarity : 0.003 0.041 2697 Dihedral : 8.372 101.838 2635 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 1.78 % Allowed : 13.35 % Favored : 84.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.19), residues: 1996 helix: 1.50 (0.15), residues: 1262 sheet: -1.78 (0.45), residues: 136 loop : -2.42 (0.25), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 485 TYR 0.009 0.001 TYR F 130 PHE 0.013 0.001 PHE G 106 TRP 0.008 0.001 TRP F 103 HIS 0.004 0.001 HIS H 75 Details of bonding type rmsd covalent geometry : bond 0.00330 (16572) covalent geometry : angle 0.50124 (22483) SS BOND : bond 0.00349 ( 4) SS BOND : angle 0.62191 ( 8) hydrogen bonds : bond 0.03292 ( 954) hydrogen bonds : angle 3.92168 ( 2802) *********************** 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 VAL 395 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 434 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 506 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 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 697 is missing expected H atoms. Skipping. Residue LYS 699 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 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 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 VAL 395 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 434 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 506 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 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 697 is missing expected H atoms. Skipping. Residue LYS 699 is missing expected H atoms. Skipping. Residue THR 784 is missing expected H atoms. Skipping. Residue SER 785 is missing expected H atoms. Skipping. Evaluate side-chains 210 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 181 time to evaluate : 0.813 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 599 ARG cc_start: 0.8805 (mtt-85) cc_final: 0.7804 (mmp80) REVERT: E 80 ILE cc_start: 0.9199 (mm) cc_final: 0.8991 (mt) REVERT: E 87 GLU cc_start: 0.7997 (mm-30) cc_final: 0.7783 (mm-30) REVERT: E 147 PHE cc_start: 0.7622 (m-10) cc_final: 0.6716 (t80) REVERT: F 22 PHE cc_start: 0.5721 (OUTLIER) cc_final: 0.4888 (t80) REVERT: F 66 LYS cc_start: 0.6649 (mtpt) cc_final: 0.6113 (mmtp) REVERT: G 33 GLU cc_start: 0.6804 (tt0) cc_final: 0.5794 (tm-30) REVERT: G 102 PHE cc_start: 0.7141 (t80) cc_final: 0.6788 (t80) REVERT: G 147 PHE cc_start: 0.7737 (m-10) cc_final: 0.6796 (t80) REVERT: H 66 LYS cc_start: 0.6648 (mtpt) cc_final: 0.6183 (mmtp) REVERT: C 599 ARG cc_start: 0.8855 (mtt-85) cc_final: 0.7843 (mmp80) REVERT: C 656 LYS cc_start: 0.8970 (OUTLIER) cc_final: 0.8538 (ptpp) outliers start: 29 outliers final: 25 residues processed: 202 average time/residue: 0.2559 time to fit residues: 80.9128 Evaluate side-chains 205 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 178 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 773 CYS Chi-restraints excluded: chain A residue 789 LEU Chi-restraints excluded: chain E residue 27 HIS Chi-restraints excluded: chain E residue 75 HIS Chi-restraints excluded: chain E residue 132 GLN Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 22 PHE Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain G residue 23 PHE Chi-restraints excluded: chain G residue 75 HIS Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain H residue 75 HIS Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain C residue 502 ILE Chi-restraints excluded: chain C residue 538 VAL Chi-restraints excluded: chain C residue 610 LEU Chi-restraints excluded: chain C residue 656 LYS Chi-restraints excluded: chain C residue 708 MET Chi-restraints excluded: chain C residue 773 CYS Chi-restraints excluded: chain C residue 789 LEU Chi-restraints excluded: chain D residue 649 THR Chi-restraints excluded: chain D residue 807 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 52 optimal weight: 5.9990 chunk 22 optimal weight: 0.9980 chunk 26 optimal weight: 3.9990 chunk 161 optimal weight: 0.9990 chunk 86 optimal weight: 4.9990 chunk 68 optimal weight: 4.9990 chunk 45 optimal weight: 0.1980 chunk 157 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 173 optimal weight: 1.9990 chunk 70 optimal weight: 8.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- 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 = 0.3896 r_free = 0.3896 target = 0.117239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.096532 restraints weight = 123935.908| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 3.29 r_work: 0.3419 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.4552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16576 Z= 0.132 Angle : 0.496 11.186 22491 Z= 0.266 Chirality : 0.053 1.373 2542 Planarity : 0.003 0.040 2697 Dihedral : 8.253 101.785 2635 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 1.47 % Allowed : 14.27 % Favored : 84.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.19), residues: 1996 helix: 1.59 (0.15), residues: 1262 sheet: -1.50 (0.48), residues: 124 loop : -2.40 (0.25), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 485 TYR 0.008 0.001 TYR E 149 PHE 0.012 0.001 PHE E 146 TRP 0.005 0.001 TRP F 103 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00293 (16572) covalent geometry : angle 0.49622 (22483) SS BOND : bond 0.00360 ( 4) SS BOND : angle 0.48020 ( 8) hydrogen bonds : bond 0.03215 ( 954) hydrogen bonds : angle 3.87549 ( 2802) *********************** 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 VAL 395 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 434 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 506 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 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 697 is missing expected H atoms. Skipping. Residue LYS 699 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 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 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 VAL 395 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 434 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 506 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 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 697 is missing expected H atoms. Skipping. Residue LYS 699 is missing expected H atoms. Skipping. Residue THR 784 is missing expected H atoms. Skipping. Residue SER 785 is missing expected H atoms. Skipping. Evaluate side-chains 205 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 181 time to evaluate : 0.989 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: A 599 ARG cc_start: 0.8825 (mtt-85) cc_final: 0.7831 (mmp80) REVERT: E 80 ILE cc_start: 0.9243 (mm) cc_final: 0.9024 (mt) REVERT: E 87 GLU cc_start: 0.7971 (mm-30) cc_final: 0.7755 (mm-30) REVERT: E 147 PHE cc_start: 0.7617 (m-10) cc_final: 0.6729 (t80) REVERT: F 66 LYS cc_start: 0.6647 (mtpt) cc_final: 0.6110 (mmtp) REVERT: G 33 GLU cc_start: 0.6810 (tt0) cc_final: 0.5795 (tm-30) REVERT: G 147 PHE cc_start: 0.7724 (m-10) cc_final: 0.6773 (t80) REVERT: H 66 LYS cc_start: 0.6635 (mtpt) cc_final: 0.6171 (mmtp) REVERT: C 599 ARG cc_start: 0.8863 (mtt-85) cc_final: 0.7945 (mmp80) REVERT: C 656 LYS cc_start: 0.8976 (OUTLIER) cc_final: 0.8539 (ptpp) outliers start: 24 outliers final: 23 residues processed: 200 average time/residue: 0.2639 time to fit residues: 81.9245 Evaluate side-chains 202 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 178 time to evaluate : 1.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 708 MET Chi-restraints excluded: chain A residue 773 CYS Chi-restraints excluded: chain A residue 789 LEU Chi-restraints excluded: chain E residue 27 HIS Chi-restraints excluded: chain E residue 75 HIS Chi-restraints excluded: chain E residue 132 GLN Chi-restraints excluded: chain F residue 75 HIS Chi-restraints excluded: chain G residue 75 HIS Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain H residue 75 HIS Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain C residue 502 ILE Chi-restraints excluded: chain C residue 538 VAL Chi-restraints excluded: chain C residue 656 LYS Chi-restraints excluded: chain C residue 708 MET Chi-restraints excluded: chain C residue 773 CYS Chi-restraints excluded: chain C residue 789 LEU Chi-restraints excluded: chain D residue 649 THR Chi-restraints excluded: chain D residue 807 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 184 optimal weight: 3.9990 chunk 67 optimal weight: 4.9990 chunk 94 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 30 optimal weight: 0.9980 chunk 168 optimal weight: 5.9990 chunk 150 optimal weight: 4.9990 chunk 56 optimal weight: 0.2980 chunk 154 optimal weight: 1.9990 chunk 186 optimal weight: 1.9990 chunk 102 optimal weight: 5.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- 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 = 0.3884 r_free = 0.3884 target = 0.116427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.095783 restraints weight = 122712.663| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 3.29 r_work: 0.3402 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.4717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 16576 Z= 0.162 Angle : 0.514 11.198 22491 Z= 0.277 Chirality : 0.053 1.374 2542 Planarity : 0.003 0.041 2697 Dihedral : 8.213 102.889 2635 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 1.65 % Allowed : 13.90 % Favored : 84.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.19), residues: 1996 helix: 1.53 (0.14), residues: 1266 sheet: -1.73 (0.47), residues: 128 loop : -2.32 (0.25), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 104 TYR 0.010 0.001 TYR F 130 PHE 0.013 0.001 PHE A 531 TRP 0.011 0.001 TRP F 103 HIS 0.003 0.001 HIS G 27 Details of bonding type rmsd covalent geometry : bond 0.00359 (16572) covalent geometry : angle 0.51395 (22483) SS BOND : bond 0.00413 ( 4) SS BOND : angle 0.68598 ( 8) hydrogen bonds : bond 0.03334 ( 954) hydrogen bonds : angle 3.93587 ( 2802) ********************** 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 VAL 395 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 434 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 506 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 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 697 is missing expected H atoms. Skipping. Residue LYS 699 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 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 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 VAL 395 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 434 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 506 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 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 697 is missing expected H atoms. Skipping. Residue LYS 699 is missing expected H atoms. Skipping. Residue THR 784 is missing expected H atoms. Skipping. Residue SER 785 is missing expected H atoms. Skipping. Evaluate side-chains 209 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 182 time to evaluate : 0.835 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: A 599 ARG cc_start: 0.8861 (mtt-85) cc_final: 0.7966 (mmp80) REVERT: E 80 ILE cc_start: 0.9238 (mm) cc_final: 0.9034 (mt) REVERT: E 87 GLU cc_start: 0.7973 (mm-30) cc_final: 0.7759 (mm-30) REVERT: E 147 PHE cc_start: 0.7690 (m-10) cc_final: 0.6778 (t80) REVERT: F 66 LYS cc_start: 0.6612 (mtpt) cc_final: 0.6077 (mmtp) REVERT: G 33 GLU cc_start: 0.6849 (tt0) cc_final: 0.5815 (tm-30) REVERT: G 147 PHE cc_start: 0.7758 (m-10) cc_final: 0.6789 (t80) REVERT: H 66 LYS cc_start: 0.6612 (mtpt) cc_final: 0.6128 (mmtp) REVERT: H 155 TYR cc_start: 0.6515 (OUTLIER) cc_final: 0.6217 (m-80) REVERT: C 599 ARG cc_start: 0.8883 (mtt-85) cc_final: 0.7983 (mmp80) REVERT: C 656 LYS cc_start: 0.8990 (OUTLIER) cc_final: 0.8554 (ptpp) REVERT: D 629 MET cc_start: 0.8429 (mtt) cc_final: 0.8125 (ttt) outliers start: 27 outliers final: 23 residues processed: 201 average time/residue: 0.2660 time to fit residues: 83.5238 Evaluate side-chains 205 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 180 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 708 MET Chi-restraints excluded: chain A residue 773 CYS Chi-restraints excluded: chain B residue 758 LEU Chi-restraints excluded: chain E residue 27 HIS Chi-restraints excluded: chain E residue 75 HIS Chi-restraints excluded: chain E residue 132 GLN Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain G residue 75 HIS Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain H residue 75 HIS Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain H residue 155 TYR Chi-restraints excluded: chain C residue 502 ILE Chi-restraints excluded: chain C residue 538 VAL Chi-restraints excluded: chain C residue 610 LEU Chi-restraints excluded: chain C residue 656 LYS Chi-restraints excluded: chain C residue 708 MET Chi-restraints excluded: chain C residue 773 CYS Chi-restraints excluded: chain C residue 789 LEU Chi-restraints excluded: chain D residue 649 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 162 optimal weight: 2.9990 chunk 97 optimal weight: 6.9990 chunk 15 optimal weight: 4.9990 chunk 122 optimal weight: 6.9990 chunk 31 optimal weight: 2.9990 chunk 182 optimal weight: 4.9990 chunk 192 optimal weight: 1.9990 chunk 77 optimal weight: 0.1980 chunk 172 optimal weight: 0.7980 chunk 69 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- 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 = 0.3878 r_free = 0.3878 target = 0.116050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.095241 restraints weight = 124675.411| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 3.29 r_work: 0.3391 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.4827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 16576 Z= 0.167 Angle : 0.516 11.203 22491 Z= 0.279 Chirality : 0.053 1.373 2542 Planarity : 0.003 0.040 2697 Dihedral : 8.156 103.632 2635 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 1.78 % Allowed : 14.27 % Favored : 83.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.19), residues: 1996 helix: 1.52 (0.14), residues: 1268 sheet: -1.76 (0.47), residues: 128 loop : -2.29 (0.25), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 104 TYR 0.010 0.001 TYR F 130 PHE 0.014 0.001 PHE G 102 TRP 0.011 0.001 TRP F 103 HIS 0.003 0.001 HIS G 27 Details of bonding type rmsd covalent geometry : bond 0.00370 (16572) covalent geometry : angle 0.51639 (22483) SS BOND : bond 0.00449 ( 4) SS BOND : angle 0.55629 ( 8) hydrogen bonds : bond 0.03362 ( 954) hydrogen bonds : angle 3.94481 ( 2802) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6824.21 seconds wall clock time: 116 minutes 46.63 seconds (7006.63 seconds total)