Starting phenix.real_space_refine on Fri Mar 6 17:39:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6peq_20330/03_2026/6peq_20330_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/6peq_20330/03_2026/6peq_20330.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6peq_20330/03_2026/6peq_20330.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6peq_20330/03_2026/6peq_20330.map" model { file = "/net/cci-nas-00/data/ceres_data/6peq_20330/03_2026/6peq_20330_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6peq_20330/03_2026/6peq_20330_trim.cif" } resolution = 2.97 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 10874 2.51 5 N 2490 2.21 5 O 2826 1.98 5 F 12 1.80 5 H 15197 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 58 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: 31523 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 5559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 380, 5559 Classifications: {'peptide': 380} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 1} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 368} Chain breaks: 2 Unresolved non-hydrogen bonds: 137 Unresolved non-hydrogen angles: 156 Unresolved non-hydrogen dihedrals: 118 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 8, 'GLN:plan1': 1, 'ASP:plan': 3, 'ARG:plan': 3, 'ASN:plan1': 3} Unresolved non-hydrogen planarities: 69 Chain: "B" Number of atoms: 5558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 5558 Classifications: {'peptide': 376} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 364} Chain breaks: 2 Unresolved non-hydrogen bonds: 125 Unresolved non-hydrogen angles: 144 Unresolved non-hydrogen dihedrals: 106 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 8, 'ASP:plan': 3, 'ARG:plan': 3, 'ASN:plan1': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 63 Chain: "E" Number of atoms: 2118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 2118 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 3, 'TRANS': 128} Chain breaks: 2 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 3, 'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "F" Number of atoms: 2185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 2185 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: 2129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 2129 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 3, 'TRANS': 128} Chain breaks: 2 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 3, 'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "H" Number of atoms: 2185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 2185 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: 5559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 380, 5559 Classifications: {'peptide': 380} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 1} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 368} Chain breaks: 2 Unresolved non-hydrogen bonds: 137 Unresolved non-hydrogen angles: 156 Unresolved non-hydrogen dihedrals: 118 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 8, 'GLN:plan1': 1, 'ASP:plan': 3, 'ARG:plan': 3, 'ASN:plan1': 3} Unresolved non-hydrogen planarities: 69 Chain: "D" Number of atoms: 5558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 5558 Classifications: {'peptide': 376} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 364} Chain breaks: 2 Unresolved non-hydrogen bonds: 125 Unresolved non-hydrogen angles: 144 Unresolved non-hydrogen dihedrals: 106 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 8, 'ASP:plan': 3, 'ARG:plan': 3, 'ASN:plan1': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 63 Chain: "A" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 106 Unusual residues: {'OLC': 1, 'PAM': 3, 'ZK1': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 131 Unusual residues: {'OLC': 2, 'PAM': 3, 'ZK1': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 46 Unusual residues: {'CLR': 1, 'PAM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 46 Unusual residues: {'CLR': 1, 'PAM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 131 Unusual residues: {'OLC': 2, 'PAM': 3, 'ZK1': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "D" Number of atoms: 156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 156 Unusual residues: {'OLC': 3, 'PAM': 3, 'ZK1': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Time building chain proxies: 6.07, per 1000 atoms: 0.19 Number of scatterers: 31523 At special positions: 0 Unit cell: (118.326, 99.138, 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 2826 8.00 N 2490 7.00 C 10874 6.00 H 15197 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: 2.86 Conformation dependent library (CDL) restraints added in 984.1 milliseconds 3992 Ramachandran restraints generated. 1996 Oldfield, 0 Emsley, 1996 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3820 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 18 sheets defined 64.8% alpha, 4.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.77 Creating SS restraints... Processing helix chain 'A' and resid 411 through 415 Processing helix chain 'A' and resid 416 through 420 Processing helix chain 'A' and resid 423 through 437 Processing helix chain 'A' and resid 461 through 469 Processing helix chain 'A' and resid 482 through 487 Processing helix chain 'A' and resid 515 through 519 Processing helix chain 'A' and resid 522 through 547 removed outlier: 3.501A pdb=" N TRP A 526 " --> pdb=" O ALA A 522 " (cutoff:3.500A) removed outlier: 3.798A 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 635 through 642 removed outlier: 3.844A pdb=" N LEU A 639 " --> pdb=" O SER A 635 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLN A 642 " --> pdb=" O ASP A 638 " (cutoff:3.500A) Processing helix chain 'A' and resid 653 through 661 Processing helix chain 'A' and resid 664 through 676 Processing helix chain 'A' and resid 685 through 696 Processing helix chain 'A' and resid 706 through 714 Processing helix chain 'A' and resid 741 through 757 removed outlier: 4.553A pdb=" N ALA A 745 " --> pdb=" O SER A 741 " (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: 3.633A pdb=" N PHE A 796 " --> pdb=" O VAL A 792 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ALA A 820 " --> pdb=" O TYR A 816 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LYS A 823 " --> pdb=" O ARG A 819 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 419 No H-bonds generated for 'chain 'B' and resid 417 through 419' Processing helix chain 'B' and resid 423 through 437 removed outlier: 3.544A 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: 3.782A pdb=" N SER B 544 " --> pdb=" O LEU B 540 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ARG B 545 " --> pdb=" O PHE B 541 " (cutoff:3.500A) Processing helix chain 'B' and resid 597 through 627 removed outlier: 3.628A pdb=" N VAL B 626 " --> pdb=" O ALA B 622 " (cutoff:3.500A) Processing helix chain 'B' and resid 635 through 642 removed outlier: 3.934A pdb=" N LEU B 639 " --> pdb=" O SER B 635 " (cutoff:3.500A) Processing helix chain 'B' and resid 653 through 661 Processing helix chain 'B' and resid 664 through 676 Processing helix chain 'B' and resid 685 through 695 Processing helix chain 'B' and resid 706 through 715 Processing helix chain 'B' and resid 742 through 757 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: 3.667A pdb=" N PHE B 796 " --> pdb=" O VAL B 792 " (cutoff:3.500A) Processing helix chain 'E' and resid 5 through 35 removed outlier: 3.739A pdb=" N CYS E 9 " --> pdb=" O PHE E 5 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ALA E 19 " --> pdb=" O VAL E 15 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N PHE E 22 " --> pdb=" O ALA E 18 " (cutoff:3.500A) Processing helix chain 'E' and resid 51 through 67 removed outlier: 4.210A pdb=" N ILE E 60 " --> pdb=" O ASN E 56 " (cutoff:3.500A) Processing helix chain 'E' and resid 68 through 85 removed outlier: 3.633A pdb=" N TYR E 72 " --> pdb=" O VAL E 68 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 107 removed outlier: 3.741A pdb=" N LEU E 91 " --> pdb=" O GLU E 87 " (cutoff:3.500A) Proline residue: E 96 - end of helix Processing helix chain 'E' and resid 127 through 158 removed outlier: 3.617A pdb=" N PHE E 147 " --> pdb=" O LEU E 143 " (cutoff:3.500A) Processing helix chain 'F' and resid 5 through 38 removed outlier: 3.903A pdb=" N CYS F 9 " --> pdb=" O PHE F 5 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 67 Processing helix chain 'F' and resid 68 through 85 removed outlier: 3.539A pdb=" N TYR F 72 " --> pdb=" O VAL F 68 " (cutoff:3.500A) Processing helix chain 'F' and resid 90 through 106 Proline residue: F 96 - end of helix removed outlier: 3.853A pdb=" N TYR F 105 " --> pdb=" O HIS F 101 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N PHE F 106 " --> pdb=" O PHE F 102 " (cutoff:3.500A) Processing helix chain 'F' and resid 127 through 158 removed outlier: 5.158A pdb=" N LYS F 133 " --> pdb=" O SER F 129 " (cutoff:3.500A) Processing helix chain 'G' and resid 5 through 35 removed outlier: 3.740A pdb=" N CYS G 9 " --> pdb=" O PHE G 5 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ALA G 19 " --> pdb=" O VAL G 15 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N PHE G 22 " --> pdb=" O ALA G 18 " (cutoff:3.500A) Processing helix chain 'G' and resid 51 through 67 removed outlier: 4.209A pdb=" N ILE G 60 " --> pdb=" O ASN G 56 " (cutoff:3.500A) Processing helix chain 'G' and resid 68 through 85 removed outlier: 3.633A pdb=" N TYR G 72 " --> pdb=" O VAL G 68 " (cutoff:3.500A) Processing helix chain 'G' and resid 87 through 107 removed outlier: 3.742A pdb=" N LEU G 91 " --> pdb=" O GLU G 87 " (cutoff:3.500A) Proline residue: G 96 - end of helix Processing helix chain 'G' and resid 127 through 158 removed outlier: 3.617A pdb=" N PHE G 147 " --> pdb=" O LEU G 143 " (cutoff:3.500A) Processing helix chain 'H' and resid 5 through 38 removed outlier: 3.904A pdb=" N CYS H 9 " --> pdb=" O PHE H 5 " (cutoff:3.500A) Processing helix chain 'H' and resid 49 through 67 Processing helix chain 'H' and resid 68 through 85 removed outlier: 3.539A pdb=" N TYR H 72 " --> pdb=" O VAL H 68 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 106 Proline residue: H 96 - end of helix removed outlier: 3.854A pdb=" N TYR H 105 " --> pdb=" O HIS H 101 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N PHE H 106 " --> pdb=" O PHE H 102 " (cutoff:3.500A) Processing helix chain 'H' and resid 127 through 158 removed outlier: 5.158A pdb=" N LYS H 133 " --> pdb=" O SER H 129 " (cutoff:3.500A) Processing helix chain 'C' and resid 411 through 415 Processing helix chain 'C' and resid 416 through 420 Processing helix chain 'C' and resid 423 through 437 Processing helix chain 'C' and resid 461 through 469 Processing helix chain 'C' and resid 482 through 487 Processing helix chain 'C' and resid 515 through 519 Processing helix chain 'C' and resid 522 through 547 removed outlier: 3.502A pdb=" N TRP C 526 " --> pdb=" O ALA C 522 " (cutoff:3.500A) removed outlier: 3.798A 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 635 through 642 removed outlier: 3.844A pdb=" N LEU C 639 " --> pdb=" O SER C 635 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLN C 642 " --> pdb=" O ASP C 638 " (cutoff:3.500A) Processing helix chain 'C' and resid 653 through 661 Processing helix chain 'C' and resid 664 through 676 Processing helix chain 'C' and resid 685 through 696 Processing helix chain 'C' and resid 706 through 714 Processing helix chain 'C' and resid 741 through 757 removed outlier: 4.553A pdb=" N ALA C 745 " --> pdb=" O SER C 741 " (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: 3.634A pdb=" N PHE C 796 " --> pdb=" O VAL C 792 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ALA C 820 " --> pdb=" O TYR C 816 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LYS C 823 " --> pdb=" O ARG C 819 " (cutoff:3.500A) Processing helix chain 'D' and resid 417 through 419 No H-bonds generated for 'chain 'D' and resid 417 through 419' Processing helix chain 'D' and resid 423 through 437 removed outlier: 3.544A 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: 3.782A pdb=" N SER D 544 " --> pdb=" O LEU D 540 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ARG D 545 " --> pdb=" O PHE D 541 " (cutoff:3.500A) Processing helix chain 'D' and resid 597 through 627 removed outlier: 3.629A pdb=" N VAL D 626 " --> pdb=" O ALA D 622 " (cutoff:3.500A) Processing helix chain 'D' and resid 635 through 642 removed outlier: 3.934A pdb=" N LEU D 639 " --> pdb=" O SER D 635 " (cutoff:3.500A) Processing helix chain 'D' and resid 653 through 661 Processing helix chain 'D' and resid 664 through 676 Processing helix chain 'D' and resid 685 through 695 Processing helix chain 'D' and resid 706 through 715 Processing helix chain 'D' and resid 742 through 757 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: 3.668A pdb=" N PHE D 796 " --> pdb=" O VAL D 792 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 440 through 444 removed outlier: 6.248A pdb=" N VAL A 395 " --> pdb=" O LYS A 441 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N THR A 443 " --> pdb=" O VAL A 395 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N VAL A 397 " --> pdb=" O THR A 443 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 407 through 408 Processing sheet with id=AA3, first strand: chain 'A' and resid 496 through 498 removed outlier: 3.741A 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: 8.567A pdb=" N TYR A 700 " --> pdb=" O LYS A 505 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N LYS A 505 " --> pdb=" O TYR A 700 " (cutoff:3.500A) removed outlier: 3.529A 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 496 through 498 removed outlier: 3.589A pdb=" N MET B 496 " --> pdb=" O TYR B 732 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 702 through 705 removed outlier: 4.070A pdb=" N ILE B 502 " --> pdb=" O VAL B 723 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 440 through 444 removed outlier: 6.248A pdb=" N VAL C 395 " --> pdb=" O LYS C 441 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N THR C 443 " --> pdb=" O VAL C 395 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N VAL C 397 " --> pdb=" O THR C 443 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 407 through 408 Processing sheet with id=AB3, first strand: chain 'C' and resid 496 through 498 removed outlier: 3.741A pdb=" N MET C 496 " --> pdb=" O TYR C 732 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 646 through 648 removed outlier: 8.566A pdb=" N TYR C 700 " --> pdb=" O LYS C 505 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N LYS C 505 " --> pdb=" O TYR C 700 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE C 504 " --> pdb=" O MET C 721 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 396 through 397 Processing sheet with id=AB6, first strand: chain 'D' and resid 407 through 408 Processing sheet with id=AB7, first strand: chain 'D' and resid 451 through 453 Processing sheet with id=AB8, first strand: chain 'D' and resid 496 through 498 removed outlier: 3.590A pdb=" N MET D 496 " --> pdb=" O TYR D 732 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 702 through 705 removed outlier: 4.069A pdb=" N ILE D 502 " --> pdb=" O VAL D 723 " (cutoff:3.500A) 994 hydrogen bonds defined for protein. 2904 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: 8.12 Time building geometry restraints manager: 3.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 15145 1.03 - 1.24: 2065 1.24 - 1.45: 5171 1.45 - 1.65: 9340 1.65 - 1.86: 184 Bond restraints: 31905 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 8.38e+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 8.34e+01 bond pdb=" CAU ZK1 D 901 " pdb=" OAB ZK1 D 901 " ideal model delta sigma weight residual 1.215 1.398 -0.183 2.00e-02 2.50e+03 8.33e+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 8.29e+01 bond pdb=" CAT ZK1 D 901 " pdb=" OAA ZK1 D 901 " ideal model delta sigma weight residual 1.214 1.396 -0.182 2.00e-02 2.50e+03 8.29e+01 ... (remaining 31900 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.36: 56961 7.36 - 14.72: 38 14.72 - 22.08: 0 22.08 - 29.44: 0 29.44 - 36.80: 6 Bond angle restraints: 57005 Sorted by residual: angle pdb=" CB ALA H 19 " pdb=" CA ALA H 19 " pdb=" HA ALA H 19 " ideal model delta sigma weight residual 109.00 72.20 36.80 3.00e+00 1.11e-01 1.51e+02 angle pdb=" N ALA H 19 " pdb=" CA ALA H 19 " pdb=" HA ALA H 19 " ideal model delta sigma weight residual 110.00 73.86 36.14 3.00e+00 1.11e-01 1.45e+02 angle pdb=" C ALA H 19 " pdb=" CA ALA H 19 " pdb=" HA ALA H 19 " ideal model delta sigma weight residual 109.00 73.60 35.40 3.00e+00 1.11e-01 1.39e+02 angle pdb=" CB LEU H 16 " pdb=" CG LEU H 16 " pdb=" HG LEU H 16 " ideal model delta sigma weight residual 109.00 78.43 30.57 3.00e+00 1.11e-01 1.04e+02 angle pdb=" CD2 LEU H 16 " pdb=" CG LEU H 16 " pdb=" HG LEU H 16 " ideal model delta sigma weight residual 108.00 77.93 30.07 3.00e+00 1.11e-01 1.00e+02 ... (remaining 57000 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.43: 15090 35.43 - 70.86: 451 70.86 - 106.30: 10 106.30 - 141.73: 12 141.73 - 177.16: 9 Dihedral angle restraints: 15572 sinusoidal: 8186 harmonic: 7386 Sorted by residual: dihedral pdb=" O23 OLC B 902 " pdb=" C22 OLC B 902 " pdb=" C24 OLC B 902 " pdb=" O25 OLC B 902 " ideal model delta sinusoidal sigma weight residual 60.48 -116.68 177.16 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C21 OLC B 902 " pdb=" C22 OLC B 902 " pdb=" C24 OLC B 902 " pdb=" O25 OLC B 902 " ideal model delta sinusoidal sigma weight residual -174.20 2.59 -176.79 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" O20 OLC A 902 " pdb=" C21 OLC A 902 " pdb=" C22 OLC A 902 " pdb=" O23 OLC A 902 " ideal model delta sinusoidal sigma weight residual 302.77 126.49 176.28 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 15569 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.147: 2532 0.147 - 0.293: 8 0.293 - 0.440: 0 0.440 - 0.586: 8 0.586 - 0.733: 2 Chirality restraints: 2550 Sorted by residual: chirality pdb=" CG LEU H 16 " pdb=" CB LEU H 16 " pdb=" CD1 LEU H 16 " pdb=" CD2 LEU H 16 " both_signs ideal model delta sigma weight residual False -2.59 -1.86 -0.73 2.00e-01 2.50e+01 1.34e+01 chirality pdb=" CG LEU F 16 " pdb=" CB LEU F 16 " pdb=" CD1 LEU F 16 " pdb=" CD2 LEU F 16 " both_signs ideal model delta sigma weight residual False -2.59 -1.86 -0.73 2.00e-01 2.50e+01 1.33e+01 chirality pdb=" C22 OLC B 902 " pdb=" C21 OLC B 902 " pdb=" C24 OLC B 902 " pdb=" O23 OLC B 902 " both_signs ideal model delta sigma weight residual False -2.31 -2.81 0.50 2.00e-01 2.50e+01 6.29e+00 ... (remaining 2547 not shown) Planarity restraints: 4660 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C10 PAM A 904 " 0.347 2.00e-02 2.50e+03 2.53e-01 6.38e+02 pdb=" C11 PAM A 904 " -0.110 2.00e-02 2.50e+03 pdb=" C8 PAM A 904 " 0.100 2.00e-02 2.50e+03 pdb=" C9 PAM A 904 " -0.336 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 PAM A 903 " 0.338 2.00e-02 2.50e+03 2.46e-01 6.04e+02 pdb=" C11 PAM A 903 " -0.111 2.00e-02 2.50e+03 pdb=" C8 PAM A 903 " 0.098 2.00e-02 2.50e+03 pdb=" C9 PAM A 903 " -0.325 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 PAM C 904 " -0.327 2.00e-02 2.50e+03 2.39e-01 5.73e+02 pdb=" C11 PAM C 904 " 0.107 2.00e-02 2.50e+03 pdb=" C8 PAM C 904 " -0.098 2.00e-02 2.50e+03 pdb=" C9 PAM C 904 " 0.318 2.00e-02 2.50e+03 ... (remaining 4657 not shown) Histogram of nonbonded interaction distances: 1.59 - 2.20: 1595 2.20 - 2.80: 63784 2.80 - 3.40: 84989 3.40 - 4.00: 108750 4.00 - 4.60: 171359 Nonbonded interactions: 430477 Sorted by model distance: nonbonded pdb=" H SER B 654 " pdb=" OAD ZK1 B 901 " model vdw 1.594 2.450 nonbonded pdb=" H SER D 654 " pdb=" OAD ZK1 D 901 " model vdw 1.604 2.450 nonbonded pdb=" O PRO A 520 " pdb="HD21 ASN A 619 " model vdw 1.609 2.450 nonbonded pdb=" O PRO C 520 " pdb="HD21 ASN C 619 " model vdw 1.611 2.450 nonbonded pdb="HH12 ARG B 485 " pdb=" OAA ZK1 B 901 " model vdw 1.614 2.450 ... (remaining 430472 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 433 or (resid 434 and (name N or name CA or na \ me C or name O or name CB or name H or name HA )) or resid 435 through 453 or (r \ esid 454 and (name N or name CA or name C or name O or name CB or name H or name \ HA )) or resid 455 or (resid 456 and (name N or name CA or name C or name O or \ name CB or name H or name HA )) or resid 457 through 633 or (resid 634 and (name \ N or name CA or name C or name O or name CB or name H or name HA )) or resid 63 \ 5 through 642 or (resid 643 through 644 and (name N or name CA or name C or name \ O or name CB or name H or name HA )) or resid 645 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 re \ sid 676 through 715 or (resid 716 and (name N or name CA or name C or name O or \ name CB or name H or name HA )) or resid 717 through 741 or (resid 742 and (name \ N or name CA or name C or name O or name CB or name H or name HA )) or resid 74 \ 3 through 751 or (resid 752 and (name N or name CA or name C or name O or name C \ B or name H or name HA )) or resid 753 through 754 or (resid 755 through 756 and \ (name N or name CA or name C or name O or name CB or name H or name HA )) or re \ sid 757 through 760 or (resid 761 and (name N or name CA or name C or name O or \ name CB or name H or name HA )) or resid 762 through 768 or (resid 769 and (name \ N or name CA or name C or name O or name CB or name H or name HA )) or resid 77 \ 0 through 774 or (resid 784 and (name N or name CA or name C or name O or name C \ B or name HA )) or (resid 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 or resid 905)) selection = (chain 'B' and ((resid 394 and (name N or name CA or name C or name O or name CB \ or name OG1 or name CG2)) or resid 395 through 505 or (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 or \ (resid 508 through 509 and (name N or name CA or name C or name O or name CB or \ name H or name HA )) or resid 510 through 637 or (resid 638 and (name N or name \ CA or name C or name O or name CB or name H or name HA )) or resid 639 through 6 \ 50 or (resid 651 through 652 and (name N or name CA or name C or name O or name \ CB or name H or name HA )) or resid 653 through 655 or (resid 656 through 657 an \ d (name N or name CA or name C or name O or name CB or name H or name HA )) or r \ esid 658 through 659 or (resid 660 and (name N or name CA or name C or name O or \ name CB or name CG or name CD or name NE or name CZ or name NH1 or name NH2 or \ name H or name HA )) or resid 661 through 662 or (resid 663 and (name N or name \ CA or name C or name O or name CB or name H or name HA )) or resid 664 through 6 \ 94 or (resid 695 and (name N or name CA or name C or name O or name CB or name H \ or name HA )) or resid 696 through 743 or (resid 744 and (name N or name CA or \ name C or name O or name CB or name H or name HA )) or resid 745 through 759 or \ (resid 760 through 761 and (name N or name CA or name C or name O or name CB or \ name H or name HA )) or resid 762 through 763 or (resid 764 and (name N or name \ CA or name C or name O or name CB or name H or name HA )) or resid 765 through 7 \ 71 or (resid 772 and (name N or name CA or name C or name O or name CB or name H \ or name HA )) or resid 773 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 thr \ ough 902 or resid 905)) selection = (chain 'C' and (resid 394 through 433 or (resid 434 and (name N or name CA or na \ me C or name O or name CB or name H or name HA )) or resid 435 through 453 or (r \ esid 454 and (name N or name CA or name C or name O or name CB or name H or name \ HA )) or resid 455 or (resid 456 and (name N or name CA or name C or name O or \ name CB or name H or name HA )) or resid 457 through 633 or (resid 634 and (name \ N or name CA or name C or name O or name CB or name H or name HA )) or resid 63 \ 5 through 642 or (resid 643 through 644 and (name N or name CA or name C or name \ O or name CB or name H or name HA )) or resid 645 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 re \ sid 676 through 715 or (resid 716 and (name N or name CA or name C or name O or \ name CB or name H or name HA )) or resid 717 through 741 or (resid 742 and (name \ N or name CA or name C or name O or name CB or name H or name HA )) or resid 74 \ 3 through 751 or (resid 752 and (name N or name CA or name C or name O or name C \ B or name H or name HA )) or resid 753 through 754 or (resid 755 through 756 and \ (name N or name CA or name C or name O or name CB or name H or name HA )) or re \ sid 757 through 760 or (resid 761 and (name N or name CA or name C or name O or \ name CB or name H or name HA )) or resid 762 through 768 or (resid 769 and (name \ N or name CA or name C or name O or name CB or name H or name HA )) or resid 77 \ 0 through 774 or (resid 784 and (name N or name CA or name C or name O or name C \ B or name HA )) or (resid 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 or resid 905)) selection = (chain 'D' and ((resid 394 and (name N or name CA or name C or name O or name CB \ or name OG1 or name CG2)) or resid 395 through 505 or (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 or \ (resid 508 through 509 and (name N or name CA or name C or name O or name CB or \ name H or name HA )) or resid 510 through 637 or (resid 638 and (name N or name \ CA or name C or name O or name CB or name H or name HA )) or resid 639 through 6 \ 50 or (resid 651 through 652 and (name N or name CA or name C or name O or name \ CB or name H or name HA )) or resid 653 through 655 or (resid 656 through 657 an \ d (name N or name CA or name C or name O or name CB or name H or name HA )) or r \ esid 658 through 659 or (resid 660 and (name N or name CA or name C or name O or \ name CB or name CG or name CD or name NE or name CZ or name NH1 or name NH2 or \ name H or name HA )) or resid 661 through 662 or (resid 663 and (name N or name \ CA or name C or name O or name CB or name H or name HA )) or resid 664 through 6 \ 94 or (resid 695 and (name N or name CA or name C or name O or name CB or name H \ or name HA )) or resid 696 through 743 or (resid 744 and (name N or name CA or \ name C or name O or name CB or name H or name HA )) or resid 745 through 759 or \ (resid 760 through 761 and (name N or name CA or name C or name O or name CB or \ name H or name HA )) or resid 762 through 763 or (resid 764 and (name N or name \ CA or name C or name O or name CB or name H or name HA )) or resid 765 through 7 \ 71 or (resid 772 and (name N or name CA or name C or name O or name CB or name H \ or name HA )) or resid 773 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 thr \ ough 902 or resid 905)) } ncs_group { reference = (chain 'E' and (resid 2 through 108 or resid 110 through 159)) selection = (chain 'F' and (resid 2 through 37 or (resid 50 and (name N or name CA or name C \ or name O or name CB or name HA or name HB1 or name HB2 or name HB3)) or (resid \ 51 through 58 and (name N or name CA or name C or name O or name CB or name H o \ r name HA )) or resid 59 through 103 or (resid 104 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 \ or name NH2 or name H or name HA )) or resid 105 through 108 or resid 125 or (r \ esid 126 and (name N or name CA or name C or name O or name CB or name HA )) or \ resid 127 through 159)) selection = (chain 'G' and (resid 2 through 103 or (resid 104 and (name N or name CA or name \ C or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 \ or name NH2 or name H or name HA )) or resid 105 through 108 or resid 110 throug \ h 159)) selection = (chain 'H' and (resid 2 through 37 or (resid 50 and (name N or name CA or name C \ or name O or name CB or name HA or name HB1 or name HB2 or name HB3)) or (resid \ 51 through 58 and (name N or name CA or name C or name O or name CB or name H o \ r name HA )) or resid 59 through 103 or (resid 104 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 \ or name NH2 or name H or name HA )) or resid 105 through 108 or resid 125 or (r \ esid 126 and (name N or name CA or name C or name O or name CB or name HA )) or \ resid 127 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: 4.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.210 Extract box with map and model: 0.540 Check model and map are aligned: 0.090 Set scattering table: 0.130 Process input model: 31.610 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:9.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 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 : 0.009 0.183 16712 Z= 0.443 Angle : 0.742 10.607 22602 Z= 0.320 Chirality : 0.051 0.733 2550 Planarity : 0.016 0.253 2700 Dihedral : 16.466 177.160 6132 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % 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: -3.10 (0.16), residues: 1996 helix: -1.01 (0.13), residues: 1234 sheet: -3.26 (0.36), residues: 168 loop : -3.75 (0.20), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 420 TYR 0.018 0.001 TYR H 148 PHE 0.011 0.001 PHE C 546 TRP 0.009 0.001 TRP H 103 HIS 0.012 0.001 HIS G 27 Details of bonding type rmsd covalent geometry : bond 0.00906 (16708) covalent geometry : angle 0.74206 (22594) SS BOND : bond 0.00159 ( 4) SS BOND : angle 0.42239 ( 8) hydrogen bonds : bond 0.12041 ( 994) hydrogen bonds : angle 6.04696 ( 2904) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3992 Ramachandran restraints generated. 1996 Oldfield, 0 Emsley, 1996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3992 Ramachandran restraints generated. 1996 Oldfield, 0 Emsley, 1996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 409 is missing expected H atoms. Skipping. Residue LYS 410 is missing expected H atoms. Skipping. Residue MET 414 is missing expected H atoms. Skipping. Residue LYS 439 is missing expected H atoms. Skipping. Residue LYS 441 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue LYS 506 is missing expected H atoms. Skipping. Residue LYS 509 is missing expected H atoms. Skipping. Residue SER 652 is missing expected H atoms. Skipping. Residue LYS 656 is missing expected H atoms. Skipping. Residue LYS 663 is missing expected H atoms. Skipping. Residue LYS 695 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 738 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 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 THR 643 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 716 is missing expected H atoms. Skipping. Residue LYS 738 is missing expected H atoms. Skipping. Residue LEU 742 is missing expected H atoms. Skipping. Residue LYS 752 is missing expected H atoms. Skipping. Residue LYS 761 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 VAL 48 is missing expected H atoms. Skipping. Residue LEU 54 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 VAL 48 is missing expected H atoms. Skipping. Residue LEU 54 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 506 is missing expected H atoms. Skipping. Residue LYS 509 is missing expected H atoms. Skipping. Residue SER 652 is missing expected H atoms. Skipping. Residue LYS 656 is missing expected H atoms. Skipping. Residue LYS 663 is missing expected H atoms. Skipping. Residue LYS 695 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 738 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 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 THR 643 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 716 is missing expected H atoms. Skipping. Residue LYS 738 is missing expected H atoms. Skipping. Residue LEU 742 is missing expected H atoms. Skipping. Residue LYS 752 is missing expected H atoms. Skipping. Residue LYS 761 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 351 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 351 time to evaluate : 1.124 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: A 670 MET cc_start: 0.9209 (mtp) cc_final: 0.8987 (mtm) REVERT: B 519 ASP cc_start: 0.8407 (m-30) cc_final: 0.8201 (m-30) REVERT: B 523 TYR cc_start: 0.7057 (m-80) cc_final: 0.6780 (m-80) REVERT: B 713 GLU cc_start: 0.8300 (tt0) cc_final: 0.7949 (tm-30) REVERT: B 726 ASN cc_start: 0.9069 (m-40) cc_final: 0.8788 (m-40) REVERT: E 23 PHE cc_start: 0.6501 (t80) cc_final: 0.6137 (t80) REVERT: E 61 CYS cc_start: 0.7564 (t) cc_final: 0.7344 (t) REVERT: E 133 LYS cc_start: 0.7221 (mttm) cc_final: 0.6506 (pttp) REVERT: F 65 ARG cc_start: 0.7886 (mtm180) cc_final: 0.7079 (mmt180) REVERT: G 133 LYS cc_start: 0.7574 (mttm) cc_final: 0.6984 (ptmm) REVERT: H 65 ARG cc_start: 0.7882 (mtm180) cc_final: 0.7092 (mmt180) REVERT: D 519 ASP cc_start: 0.8409 (m-30) cc_final: 0.8200 (m-30) REVERT: D 523 TYR cc_start: 0.7074 (m-80) cc_final: 0.6724 (m-10) REVERT: D 713 GLU cc_start: 0.8305 (tt0) cc_final: 0.7969 (tm-30) REVERT: D 726 ASN cc_start: 0.9044 (m-40) cc_final: 0.8767 (m-40) outliers start: 0 outliers final: 1 residues processed: 351 average time/residue: 1.0042 time to fit residues: 403.2117 Evaluate side-chains 207 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 206 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 80 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 98 optimal weight: 5.9990 chunk 194 optimal weight: 0.8980 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 2.9990 chunk 200 optimal weight: 0.8980 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 1.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 27 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.121574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.096363 restraints weight = 98132.682| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 2.96 r_work: 0.3320 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.2483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 16712 Z= 0.217 Angle : 0.582 10.607 22602 Z= 0.303 Chirality : 0.051 1.679 2550 Planarity : 0.004 0.036 2700 Dihedral : 14.503 161.757 2904 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 1.65 % Allowed : 13.16 % Favored : 85.19 % 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: -1.32 (0.18), residues: 1996 helix: 0.39 (0.14), residues: 1238 sheet: -2.81 (0.39), residues: 162 loop : -2.96 (0.23), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 675 TYR 0.013 0.001 TYR H 130 PHE 0.016 0.002 PHE E 62 TRP 0.006 0.001 TRP H 103 HIS 0.005 0.001 HIS E 27 Details of bonding type rmsd covalent geometry : bond 0.00491 (16708) covalent geometry : angle 0.58155 (22594) SS BOND : bond 0.00399 ( 4) SS BOND : angle 0.61679 ( 8) hydrogen bonds : bond 0.04346 ( 994) hydrogen bonds : angle 4.57209 ( 2904) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3992 Ramachandran restraints generated. 1996 Oldfield, 0 Emsley, 1996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3992 Ramachandran restraints generated. 1996 Oldfield, 0 Emsley, 1996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 409 is missing expected H atoms. Skipping. Residue LYS 410 is missing expected H atoms. Skipping. Residue MET 414 is missing expected H atoms. Skipping. Residue LYS 439 is missing expected H atoms. Skipping. Residue LYS 441 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue LYS 506 is missing expected H atoms. Skipping. Residue LYS 509 is missing expected H atoms. Skipping. Residue SER 652 is missing expected H atoms. Skipping. Residue LYS 656 is missing expected H atoms. Skipping. Residue LYS 663 is missing expected H atoms. Skipping. Residue LYS 695 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 738 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 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 THR 643 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 716 is missing expected H atoms. Skipping. Residue LYS 738 is missing expected H atoms. Skipping. Residue LEU 742 is missing expected H atoms. Skipping. Residue LYS 752 is missing expected H atoms. Skipping. Residue LYS 761 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 VAL 48 is missing expected H atoms. Skipping. Residue LEU 54 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 VAL 48 is missing expected H atoms. Skipping. Residue LEU 54 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 506 is missing expected H atoms. Skipping. Residue LYS 509 is missing expected H atoms. Skipping. Residue SER 652 is missing expected H atoms. Skipping. Residue LYS 656 is missing expected H atoms. Skipping. Residue LYS 663 is missing expected H atoms. Skipping. Residue LYS 695 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 738 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 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 THR 643 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 716 is missing expected H atoms. Skipping. Residue LYS 738 is missing expected H atoms. Skipping. Residue LEU 742 is missing expected H atoms. Skipping. Residue LYS 752 is missing expected H atoms. Skipping. Residue LYS 761 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 244 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 218 time to evaluate : 0.888 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 647 TYR cc_start: 0.8642 (p90) cc_final: 0.8372 (p90) REVERT: A 670 MET cc_start: 0.9415 (mtp) cc_final: 0.9076 (mtm) REVERT: B 503 MET cc_start: 0.8810 (ttp) cc_final: 0.8539 (ttp) REVERT: B 523 TYR cc_start: 0.7615 (m-80) cc_final: 0.7027 (m-10) REVERT: B 627 GLU cc_start: 0.8356 (tm-30) cc_final: 0.8080 (tm-30) REVERT: B 708 MET cc_start: 0.8323 (mtp) cc_final: 0.8025 (mtt) REVERT: B 713 GLU cc_start: 0.8668 (tt0) cc_final: 0.8155 (tm-30) REVERT: B 726 ASN cc_start: 0.9209 (m-40) cc_final: 0.8944 (m-40) REVERT: E 11 MET cc_start: 0.9212 (mtt) cc_final: 0.8975 (mtp) REVERT: E 31 PHE cc_start: 0.6342 (t80) cc_final: 0.6119 (t80) REVERT: E 133 LYS cc_start: 0.7274 (mttm) cc_final: 0.6437 (pttp) REVERT: F 65 ARG cc_start: 0.7843 (mtm180) cc_final: 0.7193 (mpt180) REVERT: G 23 PHE cc_start: 0.6800 (t80) cc_final: 0.6378 (t80) REVERT: G 133 LYS cc_start: 0.7663 (mttm) cc_final: 0.6912 (pttp) REVERT: H 22 PHE cc_start: 0.7936 (t80) cc_final: 0.7736 (t80) REVERT: H 65 ARG cc_start: 0.7795 (mtm180) cc_final: 0.7118 (mpt180) REVERT: C 427 ASP cc_start: 0.8569 (m-30) cc_final: 0.8354 (m-30) REVERT: C 647 TYR cc_start: 0.8565 (p90) cc_final: 0.8078 (p90) REVERT: C 670 MET cc_start: 0.9173 (mtm) cc_final: 0.8919 (mtm) REVERT: D 503 MET cc_start: 0.8833 (ttp) cc_final: 0.8585 (ttp) REVERT: D 523 TYR cc_start: 0.7649 (m-80) cc_final: 0.7422 (m-80) REVERT: D 627 GLU cc_start: 0.8391 (tm-30) cc_final: 0.8099 (tm-30) REVERT: D 713 GLU cc_start: 0.8647 (tt0) cc_final: 0.8198 (tm-30) REVERT: D 726 ASN cc_start: 0.9192 (m-40) cc_final: 0.8911 (m-40) outliers start: 26 outliers final: 11 residues processed: 230 average time/residue: 0.8851 time to fit residues: 237.2732 Evaluate side-chains 200 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 189 time to evaluate : 0.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 668 ASP Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain F residue 89 LEU Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain H residue 21 ILE Chi-restraints excluded: chain H residue 81 MET Chi-restraints excluded: chain H residue 89 LEU Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain C residue 668 ASP Chi-restraints excluded: chain D residue 498 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 178 optimal weight: 0.8980 chunk 200 optimal weight: 1.9990 chunk 116 optimal weight: 3.9990 chunk 4 optimal weight: 0.5980 chunk 48 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 196 optimal weight: 2.9990 chunk 140 optimal weight: 0.6980 chunk 89 optimal weight: 0.7980 chunk 77 optimal weight: 2.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.121873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.096520 restraints weight = 98264.767| |-----------------------------------------------------------------------------| r_work (start): 0.3445 rms_B_bonded: 2.97 r_work: 0.3319 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.2956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16712 Z= 0.132 Angle : 0.507 9.856 22602 Z= 0.262 Chirality : 0.049 1.655 2550 Planarity : 0.003 0.030 2700 Dihedral : 12.684 156.377 2902 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 2.03 % Allowed : 14.05 % Favored : 83.92 % 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: 1.28 (0.14), residues: 1228 sheet: -2.73 (0.38), residues: 168 loop : -2.62 (0.24), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 675 TYR 0.014 0.001 TYR H 151 PHE 0.011 0.001 PHE H 106 TRP 0.007 0.001 TRP H 103 HIS 0.005 0.001 HIS E 27 Details of bonding type rmsd covalent geometry : bond 0.00293 (16708) covalent geometry : angle 0.50657 (22594) SS BOND : bond 0.00213 ( 4) SS BOND : angle 0.56751 ( 8) hydrogen bonds : bond 0.03888 ( 994) hydrogen bonds : angle 4.19259 ( 2904) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3992 Ramachandran restraints generated. 1996 Oldfield, 0 Emsley, 1996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3992 Ramachandran restraints generated. 1996 Oldfield, 0 Emsley, 1996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 409 is missing expected H atoms. Skipping. Residue LYS 410 is missing expected H atoms. Skipping. Residue MET 414 is missing expected H atoms. Skipping. Residue LYS 439 is missing expected H atoms. Skipping. Residue LYS 441 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue LYS 506 is missing expected H atoms. Skipping. Residue LYS 509 is missing expected H atoms. Skipping. Residue SER 652 is missing expected H atoms. Skipping. Residue LYS 656 is missing expected H atoms. Skipping. Residue LYS 663 is missing expected H atoms. Skipping. Residue LYS 695 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 738 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 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 THR 643 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 716 is missing expected H atoms. Skipping. Residue LYS 738 is missing expected H atoms. Skipping. Residue LEU 742 is missing expected H atoms. Skipping. Residue LYS 752 is missing expected H atoms. Skipping. Residue LYS 761 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 VAL 48 is missing expected H atoms. Skipping. Residue LEU 54 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 VAL 48 is missing expected H atoms. Skipping. Residue LEU 54 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 506 is missing expected H atoms. Skipping. Residue LYS 509 is missing expected H atoms. Skipping. Residue SER 652 is missing expected H atoms. Skipping. Residue LYS 656 is missing expected H atoms. Skipping. Residue LYS 663 is missing expected H atoms. Skipping. Residue LYS 695 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 738 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 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 THR 643 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 716 is missing expected H atoms. Skipping. Residue LYS 738 is missing expected H atoms. Skipping. Residue LEU 742 is missing expected H atoms. Skipping. Residue LYS 752 is missing expected H atoms. Skipping. Residue LYS 761 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 229 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 197 time to evaluate : 0.849 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 647 TYR cc_start: 0.8727 (p90) cc_final: 0.8373 (p90) REVERT: A 670 MET cc_start: 0.9390 (mtp) cc_final: 0.9073 (mtm) REVERT: B 503 MET cc_start: 0.8729 (ttp) cc_final: 0.8487 (ttp) REVERT: B 523 TYR cc_start: 0.7607 (m-80) cc_final: 0.7031 (m-10) REVERT: B 627 GLU cc_start: 0.8338 (tm-30) cc_final: 0.8006 (tm-30) REVERT: B 629 MET cc_start: 0.8446 (mmt) cc_final: 0.8227 (tpt) REVERT: B 713 GLU cc_start: 0.8666 (tt0) cc_final: 0.8197 (tm-30) REVERT: B 726 ASN cc_start: 0.9252 (m-40) cc_final: 0.8965 (m-40) REVERT: E 80 ILE cc_start: 0.9042 (mm) cc_final: 0.8836 (mp) REVERT: E 133 LYS cc_start: 0.7250 (mttm) cc_final: 0.6460 (pttp) REVERT: F 22 PHE cc_start: 0.7640 (t80) cc_final: 0.7257 (t80) REVERT: F 65 ARG cc_start: 0.7669 (mtm180) cc_final: 0.6884 (mmt180) REVERT: G 133 LYS cc_start: 0.7524 (mttm) cc_final: 0.6770 (pttp) REVERT: H 22 PHE cc_start: 0.7936 (t80) cc_final: 0.7716 (t80) REVERT: H 65 ARG cc_start: 0.7683 (mtm180) cc_final: 0.6842 (mmt180) REVERT: C 427 ASP cc_start: 0.8580 (m-30) cc_final: 0.8333 (m-30) REVERT: C 647 TYR cc_start: 0.8627 (p90) cc_final: 0.8086 (p90) REVERT: C 670 MET cc_start: 0.9169 (mtm) cc_final: 0.8943 (mtm) REVERT: D 503 MET cc_start: 0.8741 (ttp) cc_final: 0.8520 (ttp) REVERT: D 523 TYR cc_start: 0.7634 (m-80) cc_final: 0.7005 (m-10) REVERT: D 627 GLU cc_start: 0.8273 (tm-30) cc_final: 0.7938 (tm-30) REVERT: D 629 MET cc_start: 0.8448 (mmt) cc_final: 0.8218 (tpt) REVERT: D 713 GLU cc_start: 0.8644 (tt0) cc_final: 0.8183 (tm-30) REVERT: D 726 ASN cc_start: 0.9213 (m-40) cc_final: 0.8961 (m-40) outliers start: 32 outliers final: 15 residues processed: 218 average time/residue: 0.8630 time to fit residues: 220.4558 Evaluate side-chains 205 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 190 time to evaluate : 0.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 546 PHE Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 668 ASP Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain F residue 89 LEU Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain G residue 80 ILE Chi-restraints excluded: chain H residue 21 ILE Chi-restraints excluded: chain H residue 89 LEU Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain C residue 546 PHE Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain C residue 668 ASP Chi-restraints excluded: chain D residue 498 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 71 optimal weight: 0.0670 chunk 152 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 68 optimal weight: 5.9990 chunk 161 optimal weight: 1.9990 chunk 110 optimal weight: 10.0000 chunk 177 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 chunk 12 optimal weight: 1.9990 chunk 147 optimal weight: 0.9980 chunk 55 optimal weight: 0.9990 overall best weight: 0.9322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.121514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.095760 restraints weight = 98441.613| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 2.99 r_work: 0.3308 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.3287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16712 Z= 0.135 Angle : 0.503 10.007 22602 Z= 0.262 Chirality : 0.050 1.691 2550 Planarity : 0.003 0.031 2700 Dihedral : 11.549 161.261 2902 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 2.15 % Allowed : 15.13 % Favored : 82.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.19), residues: 1996 helix: 1.61 (0.14), residues: 1246 sheet: -2.53 (0.39), residues: 168 loop : -2.48 (0.25), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 485 TYR 0.014 0.001 TYR H 151 PHE 0.045 0.001 PHE C 546 TRP 0.007 0.001 TRP H 103 HIS 0.003 0.001 HIS E 27 Details of bonding type rmsd covalent geometry : bond 0.00298 (16708) covalent geometry : angle 0.50337 (22594) SS BOND : bond 0.00227 ( 4) SS BOND : angle 0.58210 ( 8) hydrogen bonds : bond 0.03790 ( 994) hydrogen bonds : angle 4.06676 ( 2904) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3992 Ramachandran restraints generated. 1996 Oldfield, 0 Emsley, 1996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3992 Ramachandran restraints generated. 1996 Oldfield, 0 Emsley, 1996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 409 is missing expected H atoms. Skipping. Residue LYS 410 is missing expected H atoms. Skipping. Residue MET 414 is missing expected H atoms. Skipping. Residue LYS 439 is missing expected H atoms. Skipping. Residue LYS 441 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue LYS 506 is missing expected H atoms. Skipping. Residue LYS 509 is missing expected H atoms. Skipping. Residue SER 652 is missing expected H atoms. Skipping. Residue LYS 656 is missing expected H atoms. Skipping. Residue LYS 663 is missing expected H atoms. Skipping. Residue LYS 695 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 738 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 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 THR 643 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 716 is missing expected H atoms. Skipping. Residue LYS 738 is missing expected H atoms. Skipping. Residue LEU 742 is missing expected H atoms. Skipping. Residue LYS 752 is missing expected H atoms. Skipping. Residue LYS 761 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 VAL 48 is missing expected H atoms. Skipping. Residue LEU 54 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 VAL 48 is missing expected H atoms. Skipping. Residue LEU 54 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 506 is missing expected H atoms. Skipping. Residue LYS 509 is missing expected H atoms. Skipping. Residue SER 652 is missing expected H atoms. Skipping. Residue LYS 656 is missing expected H atoms. Skipping. Residue LYS 663 is missing expected H atoms. Skipping. Residue LYS 695 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 738 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 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 THR 643 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 716 is missing expected H atoms. Skipping. Residue LYS 738 is missing expected H atoms. Skipping. Residue LEU 742 is missing expected H atoms. Skipping. Residue LYS 752 is missing expected H atoms. Skipping. Residue LYS 761 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 230 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 196 time to evaluate : 0.869 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: A 627 GLU cc_start: 0.8262 (OUTLIER) cc_final: 0.7718 (mp0) REVERT: A 647 TYR cc_start: 0.8729 (p90) cc_final: 0.8353 (p90) REVERT: A 670 MET cc_start: 0.9424 (mtp) cc_final: 0.9143 (mtm) REVERT: A 821 GLU cc_start: 0.6460 (OUTLIER) cc_final: 0.6223 (pp20) REVERT: B 503 MET cc_start: 0.8810 (ttp) cc_final: 0.8591 (ttp) REVERT: B 523 TYR cc_start: 0.7637 (m-80) cc_final: 0.7039 (m-10) REVERT: B 627 GLU cc_start: 0.8270 (tm-30) cc_final: 0.7990 (tm-30) REVERT: B 713 GLU cc_start: 0.8655 (tt0) cc_final: 0.8193 (tm-30) REVERT: B 726 ASN cc_start: 0.9225 (m-40) cc_final: 0.8969 (m-40) REVERT: E 74 ILE cc_start: 0.7948 (pp) cc_final: 0.7635 (mp) REVERT: E 133 LYS cc_start: 0.7352 (mttm) cc_final: 0.6543 (pttp) REVERT: F 22 PHE cc_start: 0.7678 (t80) cc_final: 0.7297 (t80) REVERT: F 65 ARG cc_start: 0.7743 (mtm180) cc_final: 0.6908 (mmt180) REVERT: G 133 LYS cc_start: 0.7561 (mttm) cc_final: 0.6774 (pttp) REVERT: H 22 PHE cc_start: 0.7999 (t80) cc_final: 0.7772 (t80) REVERT: H 65 ARG cc_start: 0.7706 (mtm180) cc_final: 0.6840 (mmt180) REVERT: C 427 ASP cc_start: 0.8633 (m-30) cc_final: 0.8357 (m-30) REVERT: C 627 GLU cc_start: 0.8269 (OUTLIER) cc_final: 0.7703 (mp0) REVERT: C 647 TYR cc_start: 0.8579 (p90) cc_final: 0.8021 (p90) REVERT: C 670 MET cc_start: 0.9148 (mtm) cc_final: 0.8912 (mtm) REVERT: D 503 MET cc_start: 0.8829 (ttp) cc_final: 0.8616 (ttp) REVERT: D 523 TYR cc_start: 0.7627 (m-80) cc_final: 0.7009 (m-10) REVERT: D 627 GLU cc_start: 0.8236 (tm-30) cc_final: 0.7933 (tm-30) REVERT: D 713 GLU cc_start: 0.8686 (tt0) cc_final: 0.8217 (tm-30) REVERT: D 726 ASN cc_start: 0.9221 (m-40) cc_final: 0.8960 (m-40) outliers start: 34 outliers final: 17 residues processed: 217 average time/residue: 0.8572 time to fit residues: 218.3236 Evaluate side-chains 206 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 186 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 627 GLU Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 668 ASP Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 821 GLU Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain E residue 31 PHE Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain F residue 89 LEU Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain G residue 80 ILE Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain H residue 89 LEU Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain C residue 546 PHE Chi-restraints excluded: chain C residue 627 GLU Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain C residue 660 ARG Chi-restraints excluded: chain C residue 668 ASP Chi-restraints excluded: chain D residue 498 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 129 optimal weight: 10.0000 chunk 175 optimal weight: 1.9990 chunk 190 optimal weight: 3.9990 chunk 99 optimal weight: 1.9990 chunk 76 optimal weight: 3.9990 chunk 10 optimal weight: 0.8980 chunk 145 optimal weight: 1.9990 chunk 194 optimal weight: 2.9990 chunk 183 optimal weight: 0.9990 chunk 22 optimal weight: 5.9990 chunk 179 optimal weight: 1.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.119932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.093985 restraints weight = 99790.685| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 2.91 r_work: 0.3267 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.3636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 16712 Z= 0.176 Angle : 0.515 9.889 22602 Z= 0.270 Chirality : 0.050 1.688 2550 Planarity : 0.003 0.032 2700 Dihedral : 11.265 168.076 2902 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 2.78 % Allowed : 15.44 % Favored : 81.77 % 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: 0.32 (0.19), residues: 1996 helix: 1.67 (0.14), residues: 1246 sheet: -2.37 (0.39), residues: 168 loop : -2.26 (0.25), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 485 TYR 0.014 0.001 TYR F 151 PHE 0.043 0.001 PHE C 546 TRP 0.007 0.001 TRP H 103 HIS 0.004 0.001 HIS H 75 Details of bonding type rmsd covalent geometry : bond 0.00400 (16708) covalent geometry : angle 0.51453 (22594) SS BOND : bond 0.00352 ( 4) SS BOND : angle 0.78631 ( 8) hydrogen bonds : bond 0.03820 ( 994) hydrogen bonds : angle 4.05415 ( 2904) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3992 Ramachandran restraints generated. 1996 Oldfield, 0 Emsley, 1996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3992 Ramachandran restraints generated. 1996 Oldfield, 0 Emsley, 1996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 409 is missing expected H atoms. Skipping. Residue LYS 410 is missing expected H atoms. Skipping. Residue MET 414 is missing expected H atoms. Skipping. Residue LYS 439 is missing expected H atoms. Skipping. Residue LYS 441 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue LYS 506 is missing expected H atoms. Skipping. Residue LYS 509 is missing expected H atoms. Skipping. Residue SER 652 is missing expected H atoms. Skipping. Residue LYS 656 is missing expected H atoms. Skipping. Residue LYS 663 is missing expected H atoms. Skipping. Residue LYS 695 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 738 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 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 THR 643 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 716 is missing expected H atoms. Skipping. Residue LYS 738 is missing expected H atoms. Skipping. Residue LEU 742 is missing expected H atoms. Skipping. Residue LYS 752 is missing expected H atoms. Skipping. Residue LYS 761 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 VAL 48 is missing expected H atoms. Skipping. Residue LEU 54 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 VAL 48 is missing expected H atoms. Skipping. Residue LEU 54 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 506 is missing expected H atoms. Skipping. Residue LYS 509 is missing expected H atoms. Skipping. Residue SER 652 is missing expected H atoms. Skipping. Residue LYS 656 is missing expected H atoms. Skipping. Residue LYS 663 is missing expected H atoms. Skipping. Residue LYS 695 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 738 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 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 THR 643 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 716 is missing expected H atoms. Skipping. Residue LYS 738 is missing expected H atoms. Skipping. Residue LEU 742 is missing expected H atoms. Skipping. Residue LYS 752 is missing expected H atoms. Skipping. Residue LYS 761 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 239 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 195 time to evaluate : 0.974 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 627 GLU cc_start: 0.8250 (OUTLIER) cc_final: 0.7781 (mp0) REVERT: A 647 TYR cc_start: 0.8824 (p90) cc_final: 0.8472 (p90) REVERT: A 670 MET cc_start: 0.9432 (mtp) cc_final: 0.9143 (mtm) REVERT: A 798 ILE cc_start: 0.8843 (pt) cc_final: 0.8552 (mp) REVERT: A 821 GLU cc_start: 0.6457 (OUTLIER) cc_final: 0.6254 (pp20) REVERT: B 523 TYR cc_start: 0.7734 (m-80) cc_final: 0.7165 (m-10) REVERT: B 627 GLU cc_start: 0.8294 (tm-30) cc_final: 0.8056 (tm-30) REVERT: B 713 GLU cc_start: 0.8673 (tt0) cc_final: 0.8216 (tm-30) REVERT: B 726 ASN cc_start: 0.9250 (m-40) cc_final: 0.8962 (m-40) REVERT: E 80 ILE cc_start: 0.9084 (mm) cc_final: 0.8869 (OUTLIER) REVERT: E 133 LYS cc_start: 0.7362 (mttm) cc_final: 0.6497 (pttp) REVERT: F 22 PHE cc_start: 0.7685 (t80) cc_final: 0.7311 (t80) REVERT: F 65 ARG cc_start: 0.7802 (mtm180) cc_final: 0.6943 (mmt180) REVERT: F 148 TYR cc_start: 0.8348 (t80) cc_final: 0.8125 (t80) REVERT: G 133 LYS cc_start: 0.7533 (mttm) cc_final: 0.6871 (pttp) REVERT: H 11 MET cc_start: 0.8442 (mtp) cc_final: 0.8214 (mtt) REVERT: H 22 PHE cc_start: 0.8077 (t80) cc_final: 0.7847 (t80) REVERT: H 65 ARG cc_start: 0.7689 (mtm180) cc_final: 0.6836 (mmt180) REVERT: H 148 TYR cc_start: 0.8259 (t80) cc_final: 0.8028 (t80) REVERT: C 427 ASP cc_start: 0.8681 (m-30) cc_final: 0.8378 (m-30) REVERT: C 627 GLU cc_start: 0.8263 (OUTLIER) cc_final: 0.7756 (mp0) REVERT: C 670 MET cc_start: 0.9211 (mtm) cc_final: 0.8947 (mtm) REVERT: C 798 ILE cc_start: 0.8858 (pt) cc_final: 0.8562 (mp) REVERT: D 523 TYR cc_start: 0.7788 (m-80) cc_final: 0.7148 (m-80) REVERT: D 627 GLU cc_start: 0.8245 (tm-30) cc_final: 0.8015 (tm-30) REVERT: D 674 MET cc_start: 0.8205 (mtp) cc_final: 0.7999 (mtm) REVERT: D 713 GLU cc_start: 0.8726 (tt0) cc_final: 0.8244 (tm-30) REVERT: D 726 ASN cc_start: 0.9240 (m-40) cc_final: 0.8935 (m-40) outliers start: 44 outliers final: 20 residues processed: 222 average time/residue: 0.8388 time to fit residues: 218.1549 Evaluate side-chains 202 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 180 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 627 GLU Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 668 ASP Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 821 GLU Chi-restraints excluded: chain B residue 474 ILE Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 613 ILE Chi-restraints excluded: chain B residue 795 VAL Chi-restraints excluded: chain E residue 31 PHE Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain F residue 80 ILE Chi-restraints excluded: chain F residue 89 LEU Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain H residue 89 LEU Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain C residue 627 GLU Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain C residue 668 ASP Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 795 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 25 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 chunk 59 optimal weight: 0.9990 chunk 162 optimal weight: 0.9990 chunk 188 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 39 optimal weight: 4.9990 chunk 36 optimal weight: 0.4980 chunk 1 optimal weight: 3.9990 chunk 103 optimal weight: 3.9990 chunk 96 optimal weight: 1.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.120338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.094340 restraints weight = 99343.174| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 2.92 r_work: 0.3270 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.3886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16712 Z= 0.134 Angle : 0.497 9.924 22602 Z= 0.257 Chirality : 0.049 1.686 2550 Planarity : 0.003 0.031 2700 Dihedral : 10.821 169.252 2902 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 2.59 % Allowed : 16.39 % Favored : 81.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.20), residues: 1996 helix: 1.81 (0.14), residues: 1258 sheet: -2.23 (0.40), residues: 168 loop : -2.16 (0.26), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 675 TYR 0.015 0.001 TYR H 151 PHE 0.015 0.001 PHE H 106 TRP 0.007 0.001 TRP F 103 HIS 0.004 0.001 HIS F 27 Details of bonding type rmsd covalent geometry : bond 0.00301 (16708) covalent geometry : angle 0.49718 (22594) SS BOND : bond 0.00234 ( 4) SS BOND : angle 0.60543 ( 8) hydrogen bonds : bond 0.03653 ( 994) hydrogen bonds : angle 3.92206 ( 2904) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3992 Ramachandran restraints generated. 1996 Oldfield, 0 Emsley, 1996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3992 Ramachandran restraints generated. 1996 Oldfield, 0 Emsley, 1996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 409 is missing expected H atoms. Skipping. Residue LYS 410 is missing expected H atoms. Skipping. Residue MET 414 is missing expected H atoms. Skipping. Residue LYS 439 is missing expected H atoms. Skipping. Residue LYS 441 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue LYS 506 is missing expected H atoms. Skipping. Residue LYS 509 is missing expected H atoms. Skipping. Residue SER 652 is missing expected H atoms. Skipping. Residue LYS 656 is missing expected H atoms. Skipping. Residue LYS 663 is missing expected H atoms. Skipping. Residue LYS 695 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 738 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 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 THR 643 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 716 is missing expected H atoms. Skipping. Residue LYS 738 is missing expected H atoms. Skipping. Residue LEU 742 is missing expected H atoms. Skipping. Residue LYS 752 is missing expected H atoms. Skipping. Residue LYS 761 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 VAL 48 is missing expected H atoms. Skipping. Residue LEU 54 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 VAL 48 is missing expected H atoms. Skipping. Residue LEU 54 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 506 is missing expected H atoms. Skipping. Residue LYS 509 is missing expected H atoms. Skipping. Residue SER 652 is missing expected H atoms. Skipping. Residue LYS 656 is missing expected H atoms. Skipping. Residue LYS 663 is missing expected H atoms. Skipping. Residue LYS 695 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 738 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 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 THR 643 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 716 is missing expected H atoms. Skipping. Residue LYS 738 is missing expected H atoms. Skipping. Residue LEU 742 is missing expected H atoms. Skipping. Residue LYS 752 is missing expected H atoms. Skipping. Residue LYS 761 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 224 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 183 time to evaluate : 0.851 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 627 GLU cc_start: 0.8236 (OUTLIER) cc_final: 0.7801 (mp0) REVERT: A 647 TYR cc_start: 0.8851 (p90) cc_final: 0.8490 (p90) REVERT: A 670 MET cc_start: 0.9427 (mtp) cc_final: 0.9145 (mtm) REVERT: A 798 ILE cc_start: 0.8800 (pt) cc_final: 0.8560 (mp) REVERT: B 523 TYR cc_start: 0.7746 (m-80) cc_final: 0.7190 (m-80) REVERT: B 627 GLU cc_start: 0.8288 (tm-30) cc_final: 0.8048 (tm-30) REVERT: B 713 GLU cc_start: 0.8677 (tt0) cc_final: 0.8227 (tm-30) REVERT: B 726 ASN cc_start: 0.9253 (m-40) cc_final: 0.8939 (m-40) REVERT: E 133 LYS cc_start: 0.7374 (mttm) cc_final: 0.6517 (pttp) REVERT: F 22 PHE cc_start: 0.7643 (t80) cc_final: 0.7294 (t80) REVERT: F 65 ARG cc_start: 0.7798 (mtm180) cc_final: 0.6947 (mmt180) REVERT: F 148 TYR cc_start: 0.8302 (t80) cc_final: 0.8080 (t80) REVERT: G 106 PHE cc_start: 0.6217 (OUTLIER) cc_final: 0.5772 (t80) REVERT: G 133 LYS cc_start: 0.7556 (mttm) cc_final: 0.6848 (pttp) REVERT: H 11 MET cc_start: 0.8420 (mtp) cc_final: 0.8181 (mtt) REVERT: H 22 PHE cc_start: 0.8078 (t80) cc_final: 0.7862 (t80) REVERT: H 65 ARG cc_start: 0.7688 (mtm180) cc_final: 0.6871 (mmt180) REVERT: C 627 GLU cc_start: 0.8251 (OUTLIER) cc_final: 0.7777 (mp0) REVERT: C 670 MET cc_start: 0.9230 (mtm) cc_final: 0.8950 (mtm) REVERT: C 798 ILE cc_start: 0.8739 (pt) cc_final: 0.8520 (mp) REVERT: D 523 TYR cc_start: 0.7780 (m-80) cc_final: 0.7135 (m-80) REVERT: D 627 GLU cc_start: 0.8235 (tm-30) cc_final: 0.7994 (tm-30) REVERT: D 713 GLU cc_start: 0.8728 (tt0) cc_final: 0.8269 (tm-30) REVERT: D 726 ASN cc_start: 0.9247 (m-40) cc_final: 0.8926 (m-40) outliers start: 41 outliers final: 24 residues processed: 208 average time/residue: 0.8235 time to fit residues: 200.9505 Evaluate side-chains 206 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 179 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 627 GLU Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 668 ASP Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 613 ILE Chi-restraints excluded: chain B residue 795 VAL Chi-restraints excluded: chain E residue 31 PHE Chi-restraints excluded: chain E residue 106 PHE Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain F residue 89 LEU Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain G residue 106 PHE Chi-restraints excluded: chain G residue 153 MET Chi-restraints excluded: chain H residue 21 ILE Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain H residue 89 LEU Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain C residue 627 GLU Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain C residue 660 ARG Chi-restraints excluded: chain C residue 668 ASP Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 613 ILE Chi-restraints excluded: chain D residue 795 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 90 optimal weight: 3.9990 chunk 166 optimal weight: 4.9990 chunk 84 optimal weight: 0.8980 chunk 116 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 173 optimal weight: 0.4980 chunk 8 optimal weight: 0.6980 chunk 178 optimal weight: 1.9990 chunk 171 optimal weight: 4.9990 chunk 63 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.119982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.093933 restraints weight = 100163.587| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 2.92 r_work: 0.3263 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.4012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 16712 Z= 0.148 Angle : 0.501 9.948 22602 Z= 0.261 Chirality : 0.049 1.689 2550 Planarity : 0.003 0.032 2700 Dihedral : 10.440 126.763 2902 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 2.53 % Allowed : 16.27 % Favored : 81.20 % 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: 0.67 (0.20), residues: 1996 helix: 1.87 (0.14), residues: 1258 sheet: -2.18 (0.40), residues: 168 loop : -2.04 (0.27), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 675 TYR 0.014 0.001 TYR F 151 PHE 0.038 0.001 PHE E 106 TRP 0.010 0.001 TRP E 103 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00334 (16708) covalent geometry : angle 0.50073 (22594) SS BOND : bond 0.00272 ( 4) SS BOND : angle 0.64099 ( 8) hydrogen bonds : bond 0.03634 ( 994) hydrogen bonds : angle 3.90353 ( 2904) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3992 Ramachandran restraints generated. 1996 Oldfield, 0 Emsley, 1996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3992 Ramachandran restraints generated. 1996 Oldfield, 0 Emsley, 1996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 409 is missing expected H atoms. Skipping. Residue LYS 410 is missing expected H atoms. Skipping. Residue MET 414 is missing expected H atoms. Skipping. Residue LYS 439 is missing expected H atoms. Skipping. Residue LYS 441 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue LYS 506 is missing expected H atoms. Skipping. Residue LYS 509 is missing expected H atoms. Skipping. Residue SER 652 is missing expected H atoms. Skipping. Residue LYS 656 is missing expected H atoms. Skipping. Residue LYS 663 is missing expected H atoms. Skipping. Residue LYS 695 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 738 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 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 THR 643 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 716 is missing expected H atoms. Skipping. Residue LYS 738 is missing expected H atoms. Skipping. Residue LEU 742 is missing expected H atoms. Skipping. Residue LYS 752 is missing expected H atoms. Skipping. Residue LYS 761 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 VAL 48 is missing expected H atoms. Skipping. Residue LEU 54 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 VAL 48 is missing expected H atoms. Skipping. Residue LEU 54 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 506 is missing expected H atoms. Skipping. Residue LYS 509 is missing expected H atoms. Skipping. Residue SER 652 is missing expected H atoms. Skipping. Residue LYS 656 is missing expected H atoms. Skipping. Residue LYS 663 is missing expected H atoms. Skipping. Residue LYS 695 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 738 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 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 THR 643 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 716 is missing expected H atoms. Skipping. Residue LYS 738 is missing expected H atoms. Skipping. Residue LEU 742 is missing expected H atoms. Skipping. Residue LYS 752 is missing expected H atoms. Skipping. Residue LYS 761 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 222 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 182 time to evaluate : 0.851 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 627 GLU cc_start: 0.8250 (OUTLIER) cc_final: 0.7832 (mp0) REVERT: A 647 TYR cc_start: 0.8878 (p90) cc_final: 0.8506 (p90) REVERT: A 670 MET cc_start: 0.9434 (mtp) cc_final: 0.9156 (mtm) REVERT: B 523 TYR cc_start: 0.7772 (m-80) cc_final: 0.7252 (m-80) REVERT: B 627 GLU cc_start: 0.8226 (tm-30) cc_final: 0.7986 (tm-30) REVERT: B 713 GLU cc_start: 0.8679 (tt0) cc_final: 0.8231 (tm-30) REVERT: B 726 ASN cc_start: 0.9263 (m-40) cc_final: 0.8967 (m-40) REVERT: E 133 LYS cc_start: 0.7388 (mttm) cc_final: 0.6532 (pttp) REVERT: F 22 PHE cc_start: 0.7642 (t80) cc_final: 0.7299 (t80) REVERT: F 65 ARG cc_start: 0.7685 (mtm180) cc_final: 0.6866 (mmt180) REVERT: F 148 TYR cc_start: 0.8309 (t80) cc_final: 0.8105 (t80) REVERT: G 74 ILE cc_start: 0.7981 (pp) cc_final: 0.7647 (mp) REVERT: G 106 PHE cc_start: 0.6282 (OUTLIER) cc_final: 0.5829 (t80) REVERT: G 133 LYS cc_start: 0.7565 (mttm) cc_final: 0.6941 (ptmm) REVERT: H 11 MET cc_start: 0.8468 (mtp) cc_final: 0.8226 (mtt) REVERT: H 22 PHE cc_start: 0.8074 (t80) cc_final: 0.7860 (t80) REVERT: H 65 ARG cc_start: 0.7675 (mtm180) cc_final: 0.6860 (mmt180) REVERT: C 627 GLU cc_start: 0.8256 (OUTLIER) cc_final: 0.7841 (mp0) REVERT: C 670 MET cc_start: 0.9250 (mtm) cc_final: 0.8952 (mtm) REVERT: D 523 TYR cc_start: 0.7836 (m-80) cc_final: 0.7203 (m-80) REVERT: D 627 GLU cc_start: 0.8199 (tm-30) cc_final: 0.7958 (tm-30) REVERT: D 674 MET cc_start: 0.8098 (mtm) cc_final: 0.7843 (mtm) REVERT: D 713 GLU cc_start: 0.8712 (tt0) cc_final: 0.8227 (tm-30) REVERT: D 726 ASN cc_start: 0.9250 (m-40) cc_final: 0.8940 (m-40) outliers start: 40 outliers final: 24 residues processed: 208 average time/residue: 0.8017 time to fit residues: 196.1731 Evaluate side-chains 203 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 176 time to evaluate : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 627 GLU Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 668 ASP Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 613 ILE Chi-restraints excluded: chain B residue 795 VAL Chi-restraints excluded: chain E residue 31 PHE Chi-restraints excluded: chain E residue 81 MET Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain F residue 89 LEU Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain G residue 75 HIS Chi-restraints excluded: chain G residue 106 PHE Chi-restraints excluded: chain G residue 153 MET Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain H residue 89 LEU Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain C residue 479 LEU Chi-restraints excluded: chain C residue 627 GLU Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain C residue 668 ASP Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 613 ILE Chi-restraints excluded: chain D residue 795 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 127 optimal weight: 3.9990 chunk 125 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 111 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 151 optimal weight: 0.9990 chunk 180 optimal weight: 3.9990 chunk 193 optimal weight: 2.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 132 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.118609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.092268 restraints weight = 100179.706| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 2.92 r_work: 0.3234 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.4307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 16712 Z= 0.192 Angle : 0.530 9.869 22602 Z= 0.279 Chirality : 0.050 1.677 2550 Planarity : 0.003 0.032 2700 Dihedral : 10.646 115.785 2902 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 2.59 % Allowed : 16.77 % Favored : 80.63 % 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: 0.70 (0.20), residues: 1996 helix: 1.84 (0.14), residues: 1250 sheet: -2.18 (0.39), residues: 168 loop : -1.81 (0.27), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 485 TYR 0.015 0.001 TYR H 142 PHE 0.017 0.001 PHE D 531 TRP 0.005 0.001 TRP G 26 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00438 (16708) covalent geometry : angle 0.53021 (22594) SS BOND : bond 0.00411 ( 4) SS BOND : angle 0.91357 ( 8) hydrogen bonds : bond 0.03845 ( 994) hydrogen bonds : angle 3.97968 ( 2904) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3992 Ramachandran restraints generated. 1996 Oldfield, 0 Emsley, 1996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3992 Ramachandran restraints generated. 1996 Oldfield, 0 Emsley, 1996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 409 is missing expected H atoms. Skipping. Residue LYS 410 is missing expected H atoms. Skipping. Residue MET 414 is missing expected H atoms. Skipping. Residue LYS 439 is missing expected H atoms. Skipping. Residue LYS 441 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue LYS 506 is missing expected H atoms. Skipping. Residue LYS 509 is missing expected H atoms. Skipping. Residue SER 652 is missing expected H atoms. Skipping. Residue LYS 656 is missing expected H atoms. Skipping. Residue LYS 663 is missing expected H atoms. Skipping. Residue LYS 695 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 738 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 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 THR 643 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 716 is missing expected H atoms. Skipping. Residue LYS 738 is missing expected H atoms. Skipping. Residue LEU 742 is missing expected H atoms. Skipping. Residue LYS 752 is missing expected H atoms. Skipping. Residue LYS 761 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 VAL 48 is missing expected H atoms. Skipping. Residue LEU 54 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 VAL 48 is missing expected H atoms. Skipping. Residue LEU 54 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 506 is missing expected H atoms. Skipping. Residue LYS 509 is missing expected H atoms. Skipping. Residue SER 652 is missing expected H atoms. Skipping. Residue LYS 656 is missing expected H atoms. Skipping. Residue LYS 663 is missing expected H atoms. Skipping. Residue LYS 695 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 738 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 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 THR 643 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 716 is missing expected H atoms. Skipping. Residue LYS 738 is missing expected H atoms. Skipping. Residue LEU 742 is missing expected H atoms. Skipping. Residue LYS 752 is missing expected H atoms. Skipping. Residue LYS 761 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 218 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 177 time to evaluate : 0.841 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: A 627 GLU cc_start: 0.8262 (OUTLIER) cc_final: 0.7910 (mp0) REVERT: A 647 TYR cc_start: 0.8881 (p90) cc_final: 0.8543 (p90) REVERT: A 670 MET cc_start: 0.9439 (mtp) cc_final: 0.9163 (mtm) REVERT: B 713 GLU cc_start: 0.8710 (tt0) cc_final: 0.8254 (tm-30) REVERT: E 133 LYS cc_start: 0.7448 (mttm) cc_final: 0.6565 (pttp) REVERT: F 22 PHE cc_start: 0.7776 (t80) cc_final: 0.7461 (t80) REVERT: F 65 ARG cc_start: 0.7717 (mtm180) cc_final: 0.6878 (mmt180) REVERT: F 148 TYR cc_start: 0.8269 (t80) cc_final: 0.8039 (t80) REVERT: G 74 ILE cc_start: 0.8075 (pp) cc_final: 0.7779 (mp) REVERT: G 133 LYS cc_start: 0.7591 (mttm) cc_final: 0.6872 (pttp) REVERT: H 22 PHE cc_start: 0.8101 (t80) cc_final: 0.7890 (t80) REVERT: H 65 ARG cc_start: 0.7721 (mtm180) cc_final: 0.7117 (mpt180) REVERT: H 148 TYR cc_start: 0.8312 (t80) cc_final: 0.7737 (t80) REVERT: C 627 GLU cc_start: 0.8248 (OUTLIER) cc_final: 0.7895 (mp0) REVERT: C 670 MET cc_start: 0.9281 (mtm) cc_final: 0.8990 (mtm) REVERT: D 523 TYR cc_start: 0.7944 (m-80) cc_final: 0.7312 (m-80) REVERT: D 627 GLU cc_start: 0.8180 (tm-30) cc_final: 0.7954 (tm-30) REVERT: D 674 MET cc_start: 0.8098 (mtm) cc_final: 0.7847 (mtm) REVERT: D 713 GLU cc_start: 0.8750 (tt0) cc_final: 0.8267 (tm-30) outliers start: 41 outliers final: 25 residues processed: 202 average time/residue: 0.8612 time to fit residues: 203.6691 Evaluate side-chains 198 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 171 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 546 PHE Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 627 GLU Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 649 THR Chi-restraints excluded: chain A residue 668 ASP Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 613 ILE Chi-restraints excluded: chain B residue 795 VAL Chi-restraints excluded: chain E residue 31 PHE Chi-restraints excluded: chain E residue 81 MET Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain F residue 89 LEU Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain H residue 21 ILE Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain H residue 89 LEU Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain C residue 479 LEU Chi-restraints excluded: chain C residue 627 GLU Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain C residue 668 ASP Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 613 ILE Chi-restraints excluded: chain D residue 795 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 128 optimal weight: 2.9990 chunk 181 optimal weight: 0.1980 chunk 37 optimal weight: 2.9990 chunk 183 optimal weight: 0.9990 chunk 146 optimal weight: 1.9990 chunk 147 optimal weight: 2.9990 chunk 105 optimal weight: 7.9990 chunk 6 optimal weight: 5.9990 chunk 82 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 144 optimal weight: 0.5980 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 726 ASN D 726 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.118704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.092421 restraints weight = 100289.123| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 2.91 r_work: 0.3237 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.4330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.194 16712 Z= 0.202 Angle : 0.745 59.296 22602 Z= 0.418 Chirality : 0.051 1.686 2550 Planarity : 0.003 0.032 2700 Dihedral : 10.630 115.531 2902 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 2.03 % Allowed : 17.91 % Favored : 80.06 % Cbeta Deviations : 0.05 % 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: 0.70 (0.20), residues: 1996 helix: 1.85 (0.14), residues: 1250 sheet: -2.19 (0.39), residues: 168 loop : -1.82 (0.27), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 545 TYR 0.013 0.001 TYR H 151 PHE 0.044 0.002 PHE A 546 TRP 0.006 0.001 TRP G 136 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00467 (16708) covalent geometry : angle 0.74491 (22594) SS BOND : bond 0.00379 ( 4) SS BOND : angle 0.92009 ( 8) hydrogen bonds : bond 0.03818 ( 994) hydrogen bonds : angle 3.97890 ( 2904) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3992 Ramachandran restraints generated. 1996 Oldfield, 0 Emsley, 1996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3992 Ramachandran restraints generated. 1996 Oldfield, 0 Emsley, 1996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 409 is missing expected H atoms. Skipping. Residue LYS 410 is missing expected H atoms. Skipping. Residue MET 414 is missing expected H atoms. Skipping. Residue LYS 439 is missing expected H atoms. Skipping. Residue LYS 441 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue LYS 506 is missing expected H atoms. Skipping. Residue LYS 509 is missing expected H atoms. Skipping. Residue SER 652 is missing expected H atoms. Skipping. Residue LYS 656 is missing expected H atoms. Skipping. Residue LYS 663 is missing expected H atoms. Skipping. Residue LYS 695 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 738 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 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 THR 643 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 716 is missing expected H atoms. Skipping. Residue LYS 738 is missing expected H atoms. Skipping. Residue LEU 742 is missing expected H atoms. Skipping. Residue LYS 752 is missing expected H atoms. Skipping. Residue LYS 761 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 VAL 48 is missing expected H atoms. Skipping. Residue LEU 54 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 VAL 48 is missing expected H atoms. Skipping. Residue LEU 54 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 506 is missing expected H atoms. Skipping. Residue LYS 509 is missing expected H atoms. Skipping. Residue SER 652 is missing expected H atoms. Skipping. Residue LYS 656 is missing expected H atoms. Skipping. Residue LYS 663 is missing expected H atoms. Skipping. Residue LYS 695 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 738 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 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 THR 643 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 716 is missing expected H atoms. Skipping. Residue LYS 738 is missing expected H atoms. Skipping. Residue LEU 742 is missing expected H atoms. Skipping. Residue LYS 752 is missing expected H atoms. Skipping. Residue LYS 761 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 202 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 170 time to evaluate : 0.857 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 627 GLU cc_start: 0.8260 (OUTLIER) cc_final: 0.7909 (mp0) REVERT: A 647 TYR cc_start: 0.8873 (p90) cc_final: 0.8541 (p90) REVERT: A 670 MET cc_start: 0.9439 (mtp) cc_final: 0.9165 (mtm) REVERT: B 713 GLU cc_start: 0.8704 (tt0) cc_final: 0.8249 (tm-30) REVERT: E 133 LYS cc_start: 0.7448 (mttm) cc_final: 0.6566 (pttp) REVERT: F 22 PHE cc_start: 0.7770 (t80) cc_final: 0.7461 (t80) REVERT: F 65 ARG cc_start: 0.7711 (mtm180) cc_final: 0.6872 (mmt180) REVERT: F 148 TYR cc_start: 0.8275 (t80) cc_final: 0.8041 (t80) REVERT: G 74 ILE cc_start: 0.8033 (pp) cc_final: 0.7732 (mp) REVERT: G 133 LYS cc_start: 0.7591 (mttm) cc_final: 0.6871 (pttp) REVERT: H 22 PHE cc_start: 0.8095 (t80) cc_final: 0.7885 (t80) REVERT: H 65 ARG cc_start: 0.7718 (mtm180) cc_final: 0.7113 (mpt180) REVERT: H 148 TYR cc_start: 0.8305 (t80) cc_final: 0.7718 (t80) REVERT: C 627 GLU cc_start: 0.8242 (OUTLIER) cc_final: 0.7888 (mp0) REVERT: C 670 MET cc_start: 0.9282 (mtm) cc_final: 0.9001 (mtm) REVERT: D 523 TYR cc_start: 0.7940 (m-80) cc_final: 0.7308 (m-80) REVERT: D 627 GLU cc_start: 0.8172 (tm-30) cc_final: 0.7937 (tm-30) REVERT: D 674 MET cc_start: 0.8088 (mtm) cc_final: 0.7830 (mtm) REVERT: D 713 GLU cc_start: 0.8745 (tt0) cc_final: 0.8264 (tm-30) outliers start: 32 outliers final: 24 residues processed: 190 average time/residue: 0.8481 time to fit residues: 188.9802 Evaluate side-chains 195 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 169 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 627 GLU Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 668 ASP Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 613 ILE Chi-restraints excluded: chain B residue 795 VAL Chi-restraints excluded: chain E residue 31 PHE Chi-restraints excluded: chain E residue 81 MET Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain F residue 89 LEU Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain H residue 21 ILE Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain H residue 81 MET Chi-restraints excluded: chain H residue 89 LEU Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain C residue 479 LEU Chi-restraints excluded: chain C residue 627 GLU Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain C residue 668 ASP Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 613 ILE Chi-restraints excluded: chain D residue 795 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 94 optimal weight: 2.9990 chunk 136 optimal weight: 2.9990 chunk 47 optimal weight: 0.3980 chunk 91 optimal weight: 4.9990 chunk 192 optimal weight: 1.9990 chunk 104 optimal weight: 8.9990 chunk 33 optimal weight: 3.9990 chunk 85 optimal weight: 6.9990 chunk 152 optimal weight: 0.9980 chunk 46 optimal weight: 0.8980 chunk 55 optimal weight: 0.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.118752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.092465 restraints weight = 100069.826| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 2.91 r_work: 0.3237 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.4331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.194 16712 Z= 0.202 Angle : 0.745 59.296 22602 Z= 0.418 Chirality : 0.051 1.686 2550 Planarity : 0.003 0.032 2700 Dihedral : 10.630 115.531 2902 Min Nonbonded Distance : 1.635 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 1.65 % Allowed : 18.23 % Favored : 80.13 % Cbeta Deviations : 0.05 % 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: 0.70 (0.20), residues: 1996 helix: 1.85 (0.14), residues: 1250 sheet: -2.19 (0.39), residues: 168 loop : -1.82 (0.27), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 545 TYR 0.013 0.001 TYR H 151 PHE 0.044 0.002 PHE A 546 TRP 0.006 0.001 TRP G 136 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00467 (16708) covalent geometry : angle 0.74491 (22594) SS BOND : bond 0.00379 ( 4) SS BOND : angle 0.92009 ( 8) hydrogen bonds : bond 0.03818 ( 994) hydrogen bonds : angle 3.97890 ( 2904) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3992 Ramachandran restraints generated. 1996 Oldfield, 0 Emsley, 1996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3992 Ramachandran restraints generated. 1996 Oldfield, 0 Emsley, 1996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 409 is missing expected H atoms. Skipping. Residue LYS 410 is missing expected H atoms. Skipping. Residue MET 414 is missing expected H atoms. Skipping. Residue LYS 439 is missing expected H atoms. Skipping. Residue LYS 441 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue LYS 506 is missing expected H atoms. Skipping. Residue LYS 509 is missing expected H atoms. Skipping. Residue SER 652 is missing expected H atoms. Skipping. Residue LYS 656 is missing expected H atoms. Skipping. Residue LYS 663 is missing expected H atoms. Skipping. Residue LYS 695 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 738 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 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 THR 643 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 716 is missing expected H atoms. Skipping. Residue LYS 738 is missing expected H atoms. Skipping. Residue LEU 742 is missing expected H atoms. Skipping. Residue LYS 752 is missing expected H atoms. Skipping. Residue LYS 761 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 VAL 48 is missing expected H atoms. Skipping. Residue LEU 54 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 VAL 48 is missing expected H atoms. Skipping. Residue LEU 54 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 506 is missing expected H atoms. Skipping. Residue LYS 509 is missing expected H atoms. Skipping. Residue SER 652 is missing expected H atoms. Skipping. Residue LYS 656 is missing expected H atoms. Skipping. Residue LYS 663 is missing expected H atoms. Skipping. Residue LYS 695 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 738 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 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 THR 643 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 716 is missing expected H atoms. Skipping. Residue LYS 738 is missing expected H atoms. Skipping. Residue LEU 742 is missing expected H atoms. Skipping. Residue LYS 752 is missing expected H atoms. Skipping. Residue LYS 761 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 195 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 169 time to evaluate : 0.840 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 627 GLU cc_start: 0.8251 (OUTLIER) cc_final: 0.7897 (mp0) REVERT: A 647 TYR cc_start: 0.8869 (p90) cc_final: 0.8539 (p90) REVERT: A 670 MET cc_start: 0.9441 (mtp) cc_final: 0.9168 (mtm) REVERT: B 713 GLU cc_start: 0.8703 (tt0) cc_final: 0.8250 (tm-30) REVERT: E 133 LYS cc_start: 0.7447 (mttm) cc_final: 0.6564 (pttp) REVERT: F 22 PHE cc_start: 0.7776 (t80) cc_final: 0.7464 (t80) REVERT: F 65 ARG cc_start: 0.7711 (mtm180) cc_final: 0.6873 (mmt180) REVERT: F 148 TYR cc_start: 0.8274 (t80) cc_final: 0.8041 (t80) REVERT: G 74 ILE cc_start: 0.8034 (pp) cc_final: 0.7735 (mp) REVERT: G 133 LYS cc_start: 0.7593 (mttm) cc_final: 0.6872 (pttp) REVERT: H 22 PHE cc_start: 0.8094 (t80) cc_final: 0.7884 (t80) REVERT: H 65 ARG cc_start: 0.7717 (mtm180) cc_final: 0.7114 (mpt180) REVERT: H 148 TYR cc_start: 0.8307 (t80) cc_final: 0.7719 (t80) REVERT: C 627 GLU cc_start: 0.8241 (OUTLIER) cc_final: 0.7887 (mp0) REVERT: C 670 MET cc_start: 0.9277 (mtm) cc_final: 0.8998 (mtm) REVERT: D 523 TYR cc_start: 0.7939 (m-80) cc_final: 0.7306 (m-80) REVERT: D 627 GLU cc_start: 0.8182 (tm-30) cc_final: 0.7945 (tm-30) REVERT: D 674 MET cc_start: 0.8093 (mtm) cc_final: 0.7836 (mtm) REVERT: D 713 GLU cc_start: 0.8747 (tt0) cc_final: 0.8268 (tm-30) outliers start: 26 outliers final: 24 residues processed: 187 average time/residue: 0.8375 time to fit residues: 184.3099 Evaluate side-chains 195 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 169 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 627 GLU Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 668 ASP Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 613 ILE Chi-restraints excluded: chain B residue 795 VAL Chi-restraints excluded: chain E residue 31 PHE Chi-restraints excluded: chain E residue 81 MET Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain F residue 89 LEU Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain H residue 21 ILE Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain H residue 81 MET Chi-restraints excluded: chain H residue 89 LEU Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain C residue 479 LEU Chi-restraints excluded: chain C residue 627 GLU Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain C residue 668 ASP Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 613 ILE Chi-restraints excluded: chain D residue 795 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 26 optimal weight: 4.9990 chunk 83 optimal weight: 2.9990 chunk 108 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 178 optimal weight: 0.9990 chunk 159 optimal weight: 2.9990 chunk 58 optimal weight: 4.9990 chunk 44 optimal weight: 5.9990 chunk 200 optimal weight: 0.9990 chunk 144 optimal weight: 0.5980 chunk 64 optimal weight: 0.8980 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.118777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.092491 restraints weight = 100727.476| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 2.92 r_work: 0.3236 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.4332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.194 16712 Z= 0.202 Angle : 0.745 59.296 22602 Z= 0.418 Chirality : 0.051 1.686 2550 Planarity : 0.003 0.032 2700 Dihedral : 10.630 115.531 2902 Min Nonbonded Distance : 1.635 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 1.65 % Allowed : 18.29 % Favored : 80.06 % Cbeta Deviations : 0.05 % 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: 0.70 (0.20), residues: 1996 helix: 1.85 (0.14), residues: 1250 sheet: -2.19 (0.39), residues: 168 loop : -1.82 (0.27), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 545 TYR 0.013 0.001 TYR H 151 PHE 0.044 0.002 PHE A 546 TRP 0.006 0.001 TRP G 136 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00467 (16708) covalent geometry : angle 0.74491 (22594) SS BOND : bond 0.00379 ( 4) SS BOND : angle 0.92009 ( 8) hydrogen bonds : bond 0.03818 ( 994) hydrogen bonds : angle 3.97890 ( 2904) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8584.23 seconds wall clock time: 146 minutes 19.30 seconds (8779.30 seconds total)