Starting phenix.real_space_refine on Sat Jun 28 12:00:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6peq_20330/06_2025/6peq_20330_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/6peq_20330/06_2025/6peq_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_20330/06_2025/6peq_20330.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6peq_20330/06_2025/6peq_20330.map" model { file = "/net/cci-nas-00/data/ceres_data/6peq_20330/06_2025/6peq_20330_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6peq_20330/06_2025/6peq_20330_trim.cif" } resolution = 2.97 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians P 4 5.49 5 S 120 5.16 5 C 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'GLN:plan1': 1, 'GLU:plan': 8, 'ARG:plan': 3, 'ASN:plan1': 3, 'ASP:plan': 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: {'GLN:plan1': 1, 'GLU:plan': 8, 'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 3} 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: {'GLU:plan': 2, 'ARG:plan': 3, '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: {'GLU:plan': 1, 'ARG:plan': 3, 'HIS: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: {'GLU:plan': 2, 'ARG:plan': 3, '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: {'GLU:plan': 1, 'ARG:plan': 3, 'HIS: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: {'GLN:plan1': 1, 'GLU:plan': 8, 'ARG:plan': 3, 'ASN:plan1': 3, 'ASP:plan': 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: {'GLN:plan1': 1, 'GLU:plan': 8, 'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 3} 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: 17.47, per 1000 atoms: 0.55 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: 9.35 Conformation dependent library (CDL) restraints added in 2.8 seconds 3992 Ramachandran restraints generated. 1996 Oldfield, 0 Emsley, 1996 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 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: 2.67 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: 12.04 Time building geometry restraints manager: 11.06 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 824 or resid 901 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 824 or resid 901 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: 3.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.570 Extract box with map and model: 1.280 Check model and map are aligned: 0.240 Set scattering table: 0.290 Process input model: 70.610 Find NCS groups from input model: 1.420 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:18.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 96.040 ------------------------------------------------------------------------------- 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 : 6.42 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.10 (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 TRP 0.009 0.001 TRP H 103 HIS 0.012 0.001 HIS G 27 PHE 0.011 0.001 PHE C 546 TYR 0.018 0.001 TYR H 148 ARG 0.002 0.000 ARG A 420 Details of bonding type rmsd hydrogen bonds : bond 0.12041 ( 994) hydrogen bonds : angle 6.04696 ( 2904) SS BOND : bond 0.00159 ( 4) SS BOND : angle 0.42239 ( 8) covalent geometry : bond 0.00906 (16708) covalent geometry : angle 0.74206 (22594) *********************** 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 : 2.570 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: 1.9124 time to fit residues: 776.1585 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 : 2.532 ------------------------------------------------------------------------------- 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 170 optimal weight: 1.9990 chunk 153 optimal weight: 0.0020 chunk 84 optimal weight: 6.9990 chunk 52 optimal weight: 0.6980 chunk 103 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 158 optimal weight: 0.8980 chunk 61 optimal weight: 3.9990 chunk 96 optimal weight: 1.9990 chunk 117 optimal weight: 3.9990 chunk 183 optimal weight: 0.9980 overall best weight: 0.9190 ------------------------------------------------------------------------------- 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 = 0.3924 r_free = 0.3924 target = 0.124761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.100085 restraints weight = 96475.286| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 2.93 r_work: 0.3393 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.2097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16712 Z= 0.142 Angle : 0.526 10.064 22602 Z= 0.273 Chirality : 0.049 1.640 2550 Planarity : 0.003 0.035 2700 Dihedral : 14.802 170.187 2904 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 1.39 % Allowed : 12.53 % Favored : 86.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.18), residues: 1996 helix: 0.35 (0.14), residues: 1234 sheet: -3.07 (0.37), residues: 172 loop : -3.05 (0.23), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 103 HIS 0.006 0.001 HIS E 27 PHE 0.012 0.001 PHE E 62 TYR 0.011 0.001 TYR H 130 ARG 0.006 0.000 ARG C 675 Details of bonding type rmsd hydrogen bonds : bond 0.04229 ( 994) hydrogen bonds : angle 4.59844 ( 2904) SS BOND : bond 0.00227 ( 4) SS BOND : angle 0.34208 ( 8) covalent geometry : bond 0.00310 (16708) covalent geometry : angle 0.52641 (22594) *********************** 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 236 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 214 time to evaluate : 2.553 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 670 MET cc_start: 0.9376 (mtp) cc_final: 0.9048 (mtm) REVERT: B 503 MET cc_start: 0.8723 (ttp) cc_final: 0.8397 (ttp) REVERT: B 523 TYR cc_start: 0.7490 (m-80) cc_final: 0.6978 (m-10) REVERT: B 627 GLU cc_start: 0.8222 (tm-30) cc_final: 0.7829 (tm-30) REVERT: B 708 MET cc_start: 0.8315 (mtp) cc_final: 0.8002 (mtt) REVERT: B 713 GLU cc_start: 0.8557 (tt0) cc_final: 0.8046 (tm-30) REVERT: B 726 ASN cc_start: 0.9200 (m-40) cc_final: 0.8783 (m-40) REVERT: E 133 LYS cc_start: 0.7274 (mttm) cc_final: 0.6476 (pttp) REVERT: F 65 ARG cc_start: 0.7832 (mtm180) cc_final: 0.7168 (mpt180) REVERT: G 23 PHE cc_start: 0.6719 (t80) cc_final: 0.6342 (t80) REVERT: G 133 LYS cc_start: 0.7605 (mttm) cc_final: 0.6948 (ptmm) REVERT: H 65 ARG cc_start: 0.7856 (mtm180) cc_final: 0.7209 (mpt180) REVERT: C 427 ASP cc_start: 0.8557 (m-30) cc_final: 0.8344 (m-30) REVERT: C 647 TYR cc_start: 0.8559 (p90) cc_final: 0.7987 (p90) REVERT: C 670 MET cc_start: 0.9113 (mtm) cc_final: 0.8825 (mtm) REVERT: D 503 MET cc_start: 0.8682 (ttp) cc_final: 0.8368 (ttp) REVERT: D 523 TYR cc_start: 0.7519 (m-80) cc_final: 0.7196 (m-80) REVERT: D 627 GLU cc_start: 0.8148 (tm-30) cc_final: 0.7687 (tm-30) REVERT: D 713 GLU cc_start: 0.8558 (tt0) cc_final: 0.8081 (tm-30) REVERT: D 726 ASN cc_start: 0.9180 (m-40) cc_final: 0.8767 (m-40) outliers start: 22 outliers final: 11 residues processed: 223 average time/residue: 2.1517 time to fit residues: 579.3003 Evaluate side-chains 204 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 193 time to evaluate : 2.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 668 ASP 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 106 PHE 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 143 optimal weight: 1.9990 chunk 168 optimal weight: 5.9990 chunk 171 optimal weight: 7.9990 chunk 159 optimal weight: 2.9990 chunk 170 optimal weight: 2.9990 chunk 49 optimal weight: 0.5980 chunk 173 optimal weight: 1.9990 chunk 200 optimal weight: 0.4980 chunk 8 optimal weight: 2.9990 chunk 109 optimal weight: 0.7980 chunk 53 optimal weight: 4.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- 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 = 0.3886 r_free = 0.3886 target = 0.122489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.097400 restraints weight = 97759.951| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 2.97 r_work: 0.3337 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.2732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 16712 Z= 0.148 Angle : 0.510 10.078 22602 Z= 0.268 Chirality : 0.050 1.666 2550 Planarity : 0.003 0.031 2700 Dihedral : 12.892 164.643 2902 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 2.09 % Allowed : 12.97 % Favored : 84.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.19), residues: 1996 helix: 1.25 (0.14), residues: 1238 sheet: -2.90 (0.38), residues: 158 loop : -2.59 (0.24), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 103 HIS 0.005 0.001 HIS E 27 PHE 0.070 0.001 PHE G 106 TYR 0.012 0.001 TYR H 151 ARG 0.003 0.000 ARG D 485 Details of bonding type rmsd hydrogen bonds : bond 0.03937 ( 994) hydrogen bonds : angle 4.19128 ( 2904) SS BOND : bond 0.00298 ( 4) SS BOND : angle 0.71240 ( 8) covalent geometry : bond 0.00335 (16708) covalent geometry : angle 0.50987 (22594) *********************** 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 239 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 206 time to evaluate : 2.437 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 647 TYR cc_start: 0.8710 (p90) cc_final: 0.8316 (p90) REVERT: A 670 MET cc_start: 0.9392 (mtp) cc_final: 0.9157 (mtm) REVERT: A 789 LEU cc_start: 0.8956 (OUTLIER) cc_final: 0.8670 (tt) REVERT: A 821 GLU cc_start: 0.6607 (OUTLIER) cc_final: 0.6358 (pp20) REVERT: B 503 MET cc_start: 0.8733 (ttp) cc_final: 0.8471 (ttp) REVERT: B 523 TYR cc_start: 0.7541 (m-80) cc_final: 0.6986 (m-10) REVERT: B 627 GLU cc_start: 0.8319 (tm-30) cc_final: 0.7971 (tm-30) REVERT: B 708 MET cc_start: 0.8322 (mtp) cc_final: 0.8039 (mtt) REVERT: B 713 GLU cc_start: 0.8621 (tt0) cc_final: 0.8135 (tm-30) REVERT: B 726 ASN cc_start: 0.9210 (m-40) cc_final: 0.8944 (m-40) REVERT: E 11 MET cc_start: 0.9181 (mtt) cc_final: 0.8966 (mtp) REVERT: E 133 LYS cc_start: 0.7370 (mttm) cc_final: 0.6495 (pttp) REVERT: F 65 ARG cc_start: 0.7638 (mtm180) cc_final: 0.7011 (mpt180) REVERT: G 133 LYS cc_start: 0.7461 (mttm) cc_final: 0.6728 (pttp) REVERT: H 65 ARG cc_start: 0.7714 (mtm180) cc_final: 0.7072 (mpt180) REVERT: C 427 ASP cc_start: 0.8598 (m-30) cc_final: 0.8351 (m-30) REVERT: C 647 TYR cc_start: 0.8571 (p90) cc_final: 0.8001 (p90) REVERT: C 670 MET cc_start: 0.9151 (mtm) cc_final: 0.8933 (mtm) REVERT: C 789 LEU cc_start: 0.8930 (OUTLIER) cc_final: 0.8650 (tt) REVERT: C 821 GLU cc_start: 0.6631 (OUTLIER) cc_final: 0.6387 (pp20) REVERT: D 503 MET cc_start: 0.8840 (ttp) cc_final: 0.8550 (ttp) REVERT: D 523 TYR cc_start: 0.7586 (m-80) cc_final: 0.6966 (m-10) REVERT: D 627 GLU cc_start: 0.8314 (tm-30) cc_final: 0.8113 (tm-30) REVERT: D 713 GLU cc_start: 0.8602 (tt0) cc_final: 0.8127 (tm-30) REVERT: D 726 ASN cc_start: 0.9189 (m-40) cc_final: 0.8945 (m-40) outliers start: 33 outliers final: 17 residues processed: 226 average time/residue: 1.7307 time to fit residues: 462.9636 Evaluate side-chains 210 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 189 time to evaluate : 2.527 ------------------------------------------------------------------------------- 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 A residue 789 LEU Chi-restraints excluded: chain A residue 821 GLU Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 613 ILE Chi-restraints excluded: chain E residue 80 ILE Chi-restraints excluded: chain E residue 130 TYR 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 G 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 C residue 789 LEU Chi-restraints excluded: chain C residue 821 GLU Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 613 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 49 optimal weight: 0.6980 chunk 147 optimal weight: 0.5980 chunk 54 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 192 optimal weight: 3.9990 chunk 199 optimal weight: 0.5980 chunk 46 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 chunk 42 optimal weight: 0.9990 chunk 140 optimal weight: 0.8980 chunk 197 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 = 0.3895 r_free = 0.3895 target = 0.123026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.097681 restraints weight = 98221.573| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 2.97 r_work: 0.3335 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.3126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 16712 Z= 0.118 Angle : 0.493 9.875 22602 Z= 0.254 Chirality : 0.050 1.688 2550 Planarity : 0.003 0.031 2700 Dihedral : 11.639 169.872 2902 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.03 % Allowed : 14.43 % Favored : 83.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.19), residues: 1996 helix: 1.61 (0.14), residues: 1252 sheet: -2.47 (0.39), residues: 168 loop : -2.47 (0.25), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 103 HIS 0.004 0.001 HIS E 27 PHE 0.066 0.001 PHE A 546 TYR 0.014 0.001 TYR H 151 ARG 0.005 0.000 ARG A 675 Details of bonding type rmsd hydrogen bonds : bond 0.03715 ( 994) hydrogen bonds : angle 4.02021 ( 2904) SS BOND : bond 0.00187 ( 4) SS BOND : angle 0.49964 ( 8) covalent geometry : bond 0.00264 (16708) covalent geometry : angle 0.49254 (22594) *********************** 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 237 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 205 time to evaluate : 2.883 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 647 TYR cc_start: 0.8676 (p90) cc_final: 0.8304 (p90) REVERT: A 670 MET cc_start: 0.9426 (mtp) cc_final: 0.9159 (mtm) REVERT: A 789 LEU cc_start: 0.9020 (OUTLIER) cc_final: 0.8746 (tt) REVERT: B 503 MET cc_start: 0.8775 (ttp) cc_final: 0.8532 (ttp) REVERT: B 523 TYR cc_start: 0.7551 (m-80) cc_final: 0.6962 (m-10) REVERT: B 627 GLU cc_start: 0.8285 (tm-30) cc_final: 0.7993 (tm-30) REVERT: B 708 MET cc_start: 0.8352 (mtp) cc_final: 0.8148 (mtt) REVERT: B 713 GLU cc_start: 0.8631 (tt0) cc_final: 0.8174 (tm-30) REVERT: B 726 ASN cc_start: 0.9216 (m-40) cc_final: 0.8965 (m-40) REVERT: E 74 ILE cc_start: 0.7917 (pp) cc_final: 0.7611 (mp) REVERT: E 133 LYS cc_start: 0.7319 (mttm) cc_final: 0.6476 (pttp) REVERT: F 65 ARG cc_start: 0.7714 (mtm180) cc_final: 0.6894 (mmt180) REVERT: G 133 LYS cc_start: 0.7487 (mttm) cc_final: 0.6882 (ptmm) REVERT: H 22 PHE cc_start: 0.7768 (t80) cc_final: 0.7405 (t80) REVERT: H 65 ARG cc_start: 0.7705 (mtm180) cc_final: 0.6847 (mmt180) REVERT: C 427 ASP cc_start: 0.8585 (m-30) cc_final: 0.8326 (m-30) REVERT: C 627 GLU cc_start: 0.8307 (OUTLIER) cc_final: 0.7764 (mp0) REVERT: C 647 TYR cc_start: 0.8534 (p90) cc_final: 0.7996 (p90) REVERT: C 670 MET cc_start: 0.9144 (mtm) cc_final: 0.8936 (mtm) REVERT: C 789 LEU cc_start: 0.8994 (OUTLIER) cc_final: 0.8766 (tt) REVERT: D 503 MET cc_start: 0.8786 (ttp) cc_final: 0.8554 (ttp) REVERT: D 523 TYR cc_start: 0.7569 (m-80) cc_final: 0.6975 (m-10) REVERT: D 627 GLU cc_start: 0.8180 (tm-30) cc_final: 0.7902 (tm-30) REVERT: D 713 GLU cc_start: 0.8651 (tt0) cc_final: 0.8158 (tm-30) REVERT: D 726 ASN cc_start: 0.9209 (m-40) cc_final: 0.8943 (m-40) outliers start: 32 outliers final: 17 residues processed: 221 average time/residue: 2.1964 time to fit residues: 581.1667 Evaluate side-chains 211 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 191 time to evaluate : 3.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 546 PHE Chi-restraints excluded: chain A residue 668 ASP Chi-restraints excluded: chain A residue 789 LEU Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain E residue 80 ILE Chi-restraints excluded: chain E residue 130 TYR Chi-restraints excluded: chain F residue 21 ILE 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 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 627 GLU Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain C residue 668 ASP Chi-restraints excluded: chain C residue 789 LEU 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 28 optimal weight: 0.8980 chunk 106 optimal weight: 8.9990 chunk 152 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 40 optimal weight: 10.0000 chunk 43 optimal weight: 1.9990 chunk 168 optimal weight: 0.8980 chunk 66 optimal weight: 3.9990 chunk 55 optimal weight: 0.9990 chunk 92 optimal weight: 1.9990 chunk 47 optimal weight: 0.5980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 709 ASN 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 = 0.121816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.096153 restraints weight = 98632.669| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 2.98 r_work: 0.3311 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.3387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16712 Z= 0.135 Angle : 0.484 9.959 22602 Z= 0.252 Chirality : 0.049 1.690 2550 Planarity : 0.003 0.032 2700 Dihedral : 10.854 152.926 2902 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 2.15 % Allowed : 15.00 % Favored : 82.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.20), residues: 1996 helix: 1.76 (0.15), residues: 1254 sheet: -2.31 (0.39), residues: 168 loop : -2.29 (0.26), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 103 HIS 0.004 0.001 HIS E 27 PHE 0.072 0.001 PHE C 546 TYR 0.014 0.001 TYR H 151 ARG 0.002 0.000 ARG D 485 Details of bonding type rmsd hydrogen bonds : bond 0.03637 ( 994) hydrogen bonds : angle 3.92927 ( 2904) SS BOND : bond 0.00242 ( 4) SS BOND : angle 0.60298 ( 8) covalent geometry : bond 0.00298 (16708) covalent geometry : angle 0.48374 (22594) *********************** 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 227 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 193 time to evaluate : 2.797 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: A 627 GLU cc_start: 0.8278 (OUTLIER) cc_final: 0.7761 (mp0) REVERT: A 647 TYR cc_start: 0.8705 (p90) cc_final: 0.8372 (p90) REVERT: A 670 MET cc_start: 0.9413 (mtp) cc_final: 0.9149 (mtm) REVERT: A 798 ILE cc_start: 0.8881 (pp) cc_final: 0.8627 (mp) REVERT: B 503 MET cc_start: 0.8813 (ttp) cc_final: 0.8578 (ttp) REVERT: B 523 TYR cc_start: 0.7625 (m-80) cc_final: 0.7034 (m-10) REVERT: B 627 GLU cc_start: 0.8250 (tm-30) cc_final: 0.8024 (tm-30) REVERT: B 674 MET cc_start: 0.8032 (mtt) cc_final: 0.7832 (mtm) REVERT: B 713 GLU cc_start: 0.8624 (tt0) cc_final: 0.8176 (tm-30) REVERT: B 726 ASN cc_start: 0.9236 (m-40) cc_final: 0.8957 (m-40) REVERT: E 74 ILE cc_start: 0.7910 (pp) cc_final: 0.7709 (mp) REVERT: E 133 LYS cc_start: 0.7287 (mttm) cc_final: 0.6466 (pttp) REVERT: F 22 PHE cc_start: 0.7799 (t80) cc_final: 0.7487 (t80) REVERT: F 65 ARG cc_start: 0.7767 (mtm180) cc_final: 0.6947 (mmt180) REVERT: G 11 MET cc_start: 0.9216 (mtm) cc_final: 0.8993 (mtp) REVERT: G 133 LYS cc_start: 0.7477 (mttm) cc_final: 0.6741 (pttp) REVERT: H 22 PHE cc_start: 0.7657 (t80) cc_final: 0.7314 (t80) REVERT: H 65 ARG cc_start: 0.7691 (mtm180) cc_final: 0.6838 (mmt180) REVERT: C 427 ASP cc_start: 0.8652 (m-30) cc_final: 0.8360 (m-30) REVERT: C 627 GLU cc_start: 0.8288 (OUTLIER) cc_final: 0.7671 (mp0) REVERT: C 647 TYR cc_start: 0.8563 (p90) cc_final: 0.7987 (p90) REVERT: C 670 MET cc_start: 0.9171 (mtm) cc_final: 0.8945 (mtm) REVERT: C 789 LEU cc_start: 0.9028 (OUTLIER) cc_final: 0.8791 (tt) REVERT: C 798 ILE cc_start: 0.8863 (pp) cc_final: 0.8620 (mp) REVERT: D 503 MET cc_start: 0.8799 (ttp) cc_final: 0.8570 (ttp) REVERT: D 523 TYR cc_start: 0.7626 (m-80) cc_final: 0.6995 (m-10) REVERT: D 627 GLU cc_start: 0.8181 (tm-30) cc_final: 0.7916 (tm-30) REVERT: D 674 MET cc_start: 0.8148 (OUTLIER) cc_final: 0.7939 (mtm) REVERT: D 713 GLU cc_start: 0.8635 (tt0) cc_final: 0.8150 (tm-30) REVERT: D 726 ASN cc_start: 0.9217 (m-40) cc_final: 0.8927 (m-40) outliers start: 34 outliers final: 16 residues processed: 208 average time/residue: 1.6803 time to fit residues: 417.4337 Evaluate side-chains 209 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 189 time to evaluate : 2.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 627 GLU Chi-restraints excluded: chain A residue 668 ASP Chi-restraints excluded: chain A residue 789 LEU Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain E residue 80 ILE Chi-restraints excluded: chain E residue 130 TYR Chi-restraints excluded: chain F residue 21 ILE 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 627 GLU Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain C residue 668 ASP Chi-restraints excluded: chain C residue 789 LEU Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 674 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 118 optimal weight: 10.0000 chunk 127 optimal weight: 3.9990 chunk 28 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 74 optimal weight: 3.9990 chunk 154 optimal weight: 2.9990 chunk 167 optimal weight: 10.0000 chunk 178 optimal weight: 0.8980 chunk 52 optimal weight: 1.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- 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 = 0.3813 r_free = 0.3813 target = 0.117766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.091513 restraints weight = 100639.668| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 2.91 r_work: 0.3222 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.3994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.086 16712 Z= 0.249 Angle : 0.578 10.089 22602 Z= 0.309 Chirality : 0.052 1.685 2550 Planarity : 0.004 0.036 2700 Dihedral : 11.344 136.396 2902 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.61 % Favored : 94.34 % Rotamer: Outliers : 3.10 % Allowed : 15.44 % Favored : 81.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.19), residues: 1996 helix: 1.40 (0.14), residues: 1256 sheet: -2.31 (0.40), residues: 168 loop : -2.14 (0.27), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 26 HIS 0.006 0.001 HIS F 75 PHE 0.019 0.002 PHE B 531 TYR 0.014 0.002 TYR H 100 ARG 0.003 0.000 ARG C 545 Details of bonding type rmsd hydrogen bonds : bond 0.04245 ( 994) hydrogen bonds : angle 4.20019 ( 2904) SS BOND : bond 0.00575 ( 4) SS BOND : angle 1.25917 ( 8) covalent geometry : bond 0.00568 (16708) covalent geometry : angle 0.57792 (22594) *********************** 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 238 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 189 time to evaluate : 2.582 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: 0.8286 (OUTLIER) cc_final: 0.7931 (mp0) REVERT: A 647 TYR cc_start: 0.8868 (p90) cc_final: 0.8431 (p90) REVERT: A 670 MET cc_start: 0.9418 (mtp) cc_final: 0.9122 (mtm) REVERT: B 503 MET cc_start: 0.8918 (ttp) cc_final: 0.8710 (ttp) REVERT: B 627 GLU cc_start: 0.8355 (tm-30) cc_final: 0.8104 (tm-30) REVERT: B 713 GLU cc_start: 0.8698 (tt0) cc_final: 0.8249 (tm-30) REVERT: E 133 LYS cc_start: 0.7330 (mttm) cc_final: 0.6480 (pttp) REVERT: F 22 PHE cc_start: 0.7761 (t80) cc_final: 0.7439 (t80) REVERT: F 65 ARG cc_start: 0.7675 (mtm180) cc_final: 0.6862 (mmt180) REVERT: F 148 TYR cc_start: 0.8327 (t80) cc_final: 0.8106 (t80) REVERT: G 133 LYS cc_start: 0.7537 (mttm) cc_final: 0.6831 (pttp) REVERT: H 22 PHE cc_start: 0.7749 (t80) cc_final: 0.7450 (t80) REVERT: H 65 ARG cc_start: 0.7697 (mtm180) cc_final: 0.6862 (mmt180) REVERT: H 148 TYR cc_start: 0.8317 (t80) cc_final: 0.8096 (t80) REVERT: C 427 ASP cc_start: 0.8691 (m-30) cc_final: 0.8380 (m-30) REVERT: C 627 GLU cc_start: 0.8278 (OUTLIER) cc_final: 0.7906 (mp0) REVERT: C 670 MET cc_start: 0.9231 (mtm) cc_final: 0.8979 (mtm) REVERT: D 503 MET cc_start: 0.8922 (ttp) cc_final: 0.8715 (ttp) REVERT: D 523 TYR cc_start: 0.7961 (m-80) cc_final: 0.7369 (m-80) REVERT: D 674 MET cc_start: 0.8159 (OUTLIER) cc_final: 0.7941 (mtm) REVERT: D 713 GLU cc_start: 0.8795 (tt0) cc_final: 0.8305 (tm-30) outliers start: 49 outliers final: 21 residues processed: 222 average time/residue: 1.6516 time to fit residues: 433.4697 Evaluate side-chains 193 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 169 time to evaluate : 2.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 627 GLU Chi-restraints excluded: chain A residue 668 ASP Chi-restraints excluded: chain A residue 789 LEU Chi-restraints excluded: chain B residue 474 ILE Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain E residue 80 ILE Chi-restraints excluded: chain E residue 106 PHE Chi-restraints excluded: chain E residue 130 TYR 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 F residue 150 LEU Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain H residue 80 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 627 GLU Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain C residue 668 ASP Chi-restraints excluded: chain C residue 789 LEU Chi-restraints excluded: chain D residue 474 ILE Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 674 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 166 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 109 optimal weight: 5.9990 chunk 179 optimal weight: 0.9980 chunk 58 optimal weight: 3.9990 chunk 185 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 6 optimal weight: 5.9990 chunk 7 optimal weight: 0.9990 chunk 200 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- 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 = 0.3813 r_free = 0.3813 target = 0.117959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.091735 restraints weight = 100721.893| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 2.92 r_work: 0.3223 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.4204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 16712 Z= 0.209 Angle : 0.546 9.961 22602 Z= 0.289 Chirality : 0.051 1.684 2550 Planarity : 0.004 0.058 2700 Dihedral : 10.970 126.944 2902 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 2.53 % Allowed : 16.71 % Favored : 80.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.19), residues: 1996 helix: 1.53 (0.14), residues: 1256 sheet: -2.20 (0.39), residues: 168 loop : -2.06 (0.27), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 103 HIS 0.005 0.001 HIS F 75 PHE 0.021 0.002 PHE E 106 TYR 0.014 0.001 TYR H 142 ARG 0.011 0.000 ARG A 675 Details of bonding type rmsd hydrogen bonds : bond 0.03980 ( 994) hydrogen bonds : angle 4.08184 ( 2904) SS BOND : bond 0.00412 ( 4) SS BOND : angle 0.91772 ( 8) covalent geometry : bond 0.00475 (16708) covalent geometry : angle 0.54542 (22594) *********************** 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 216 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 176 time to evaluate : 2.485 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: A 627 GLU cc_start: 0.8271 (OUTLIER) cc_final: 0.7936 (mp0) REVERT: A 647 TYR cc_start: 0.8868 (p90) cc_final: 0.8440 (p90) REVERT: A 670 MET cc_start: 0.9423 (mtp) cc_final: 0.9112 (mtm) REVERT: B 674 MET cc_start: 0.8207 (mtm) cc_final: 0.7935 (mtm) REVERT: B 713 GLU cc_start: 0.8687 (tt0) cc_final: 0.8256 (tm-30) REVERT: E 133 LYS cc_start: 0.7337 (mttm) cc_final: 0.6488 (pttp) REVERT: F 22 PHE cc_start: 0.7840 (t80) cc_final: 0.7506 (t80) REVERT: F 65 ARG cc_start: 0.7728 (mtm180) cc_final: 0.6886 (mmt180) REVERT: G 74 ILE cc_start: 0.8011 (pp) cc_final: 0.7691 (mp) REVERT: G 133 LYS cc_start: 0.7562 (mttm) cc_final: 0.6928 (ptmm) REVERT: H 22 PHE cc_start: 0.7782 (t80) cc_final: 0.7475 (t80) REVERT: H 65 ARG cc_start: 0.7698 (mtm180) cc_final: 0.7070 (mpt180) REVERT: C 627 GLU cc_start: 0.8265 (OUTLIER) cc_final: 0.7917 (mp0) REVERT: C 670 MET cc_start: 0.9254 (mtm) cc_final: 0.8960 (mtm) REVERT: D 523 TYR cc_start: 0.7967 (m-80) cc_final: 0.7357 (m-80) REVERT: D 674 MET cc_start: 0.8197 (OUTLIER) cc_final: 0.7980 (mtm) REVERT: D 713 GLU cc_start: 0.8782 (tt0) cc_final: 0.8305 (tm-30) outliers start: 40 outliers final: 18 residues processed: 201 average time/residue: 1.6622 time to fit residues: 396.8821 Evaluate side-chains 187 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 166 time to evaluate : 2.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 627 GLU Chi-restraints excluded: chain A residue 668 ASP Chi-restraints excluded: chain A residue 789 LEU Chi-restraints excluded: chain B residue 474 ILE Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain E residue 80 ILE Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain F residue 81 MET Chi-restraints excluded: chain F residue 89 LEU Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain G residue 152 CYS Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain H residue 80 ILE 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 C residue 789 LEU Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 674 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 36 optimal weight: 2.9990 chunk 189 optimal weight: 2.9990 chunk 175 optimal weight: 1.9990 chunk 111 optimal weight: 5.9990 chunk 142 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 16 optimal weight: 0.2980 chunk 71 optimal weight: 2.9990 chunk 196 optimal weight: 2.9990 overall best weight: 1.6588 ------------------------------------------------------------------------------- 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 = 0.3815 r_free = 0.3815 target = 0.118151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.091847 restraints weight = 100661.693| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 2.92 r_work: 0.3225 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.4385 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= 0.183 Angle : 0.542 9.970 22602 Z= 0.285 Chirality : 0.050 1.683 2550 Planarity : 0.003 0.036 2700 Dihedral : 10.786 117.199 2902 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 2.15 % Allowed : 17.85 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.19), residues: 1996 helix: 1.68 (0.14), residues: 1254 sheet: -2.14 (0.39), residues: 168 loop : -2.05 (0.27), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP G 136 HIS 0.005 0.001 HIS G 27 PHE 0.023 0.001 PHE C 546 TYR 0.018 0.001 TYR C 647 ARG 0.008 0.000 ARG A 675 Details of bonding type rmsd hydrogen bonds : bond 0.03897 ( 994) hydrogen bonds : angle 4.03082 ( 2904) SS BOND : bond 0.00355 ( 4) SS BOND : angle 0.93523 ( 8) covalent geometry : bond 0.00416 (16708) covalent geometry : angle 0.54182 (22594) *********************** 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 204 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 170 time to evaluate : 2.412 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: A 627 GLU cc_start: 0.8263 (OUTLIER) cc_final: 0.7918 (mp0) REVERT: A 647 TYR cc_start: 0.8849 (p90) cc_final: 0.8437 (p90) REVERT: A 670 MET cc_start: 0.9405 (mtp) cc_final: 0.9119 (mtm) REVERT: B 674 MET cc_start: 0.8168 (mtm) cc_final: 0.7893 (mtm) REVERT: B 713 GLU cc_start: 0.8675 (tt0) cc_final: 0.8247 (tm-30) REVERT: E 133 LYS cc_start: 0.7350 (mttm) cc_final: 0.6508 (pttp) REVERT: F 22 PHE cc_start: 0.7748 (t80) cc_final: 0.7407 (t80) REVERT: F 65 ARG cc_start: 0.7720 (mtm180) cc_final: 0.6917 (mmt180) REVERT: G 74 ILE cc_start: 0.7979 (pp) cc_final: 0.7721 (mp) REVERT: G 133 LYS cc_start: 0.7574 (mttm) cc_final: 0.6805 (pttp) REVERT: H 22 PHE cc_start: 0.7804 (t80) cc_final: 0.7492 (t80) REVERT: H 65 ARG cc_start: 0.7749 (mtm180) cc_final: 0.6965 (mmt180) REVERT: C 627 GLU cc_start: 0.8241 (OUTLIER) cc_final: 0.7888 (mp0) REVERT: C 670 MET cc_start: 0.9235 (mtm) cc_final: 0.8981 (mtm) REVERT: D 523 TYR cc_start: 0.7968 (m-80) cc_final: 0.7334 (m-80) REVERT: D 674 MET cc_start: 0.8218 (OUTLIER) cc_final: 0.8014 (mtm) REVERT: D 713 GLU cc_start: 0.8777 (tt0) cc_final: 0.8299 (tm-30) outliers start: 34 outliers final: 19 residues processed: 194 average time/residue: 1.6072 time to fit residues: 370.5895 Evaluate side-chains 188 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 166 time to evaluate : 2.322 ------------------------------------------------------------------------------- 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 789 LEU Chi-restraints excluded: chain B residue 474 ILE Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain E residue 80 ILE Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain F residue 81 MET 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 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 627 GLU Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain C residue 668 ASP Chi-restraints excluded: chain C residue 789 LEU Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 674 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 51 optimal weight: 1.9990 chunk 84 optimal weight: 0.4980 chunk 48 optimal weight: 1.9990 chunk 180 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 179 optimal weight: 0.5980 chunk 127 optimal weight: 3.9990 chunk 106 optimal weight: 3.9990 chunk 113 optimal weight: 2.9990 chunk 143 optimal weight: 1.9990 chunk 169 optimal weight: 7.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- 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 = 0.3821 r_free = 0.3821 target = 0.118496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.092255 restraints weight = 100311.894| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 2.91 r_work: 0.3233 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.4486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 16712 Z= 0.163 Angle : 0.532 9.920 22602 Z= 0.277 Chirality : 0.050 1.682 2550 Planarity : 0.003 0.035 2700 Dihedral : 10.560 114.449 2902 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 1.90 % Allowed : 18.23 % Favored : 79.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.20), residues: 1996 helix: 1.77 (0.14), residues: 1256 sheet: -2.08 (0.40), residues: 168 loop : -2.00 (0.27), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP G 136 HIS 0.005 0.001 HIS G 27 PHE 0.025 0.001 PHE C 546 TYR 0.019 0.001 TYR F 142 ARG 0.008 0.000 ARG A 675 Details of bonding type rmsd hydrogen bonds : bond 0.03788 ( 994) hydrogen bonds : angle 3.95768 ( 2904) SS BOND : bond 0.00300 ( 4) SS BOND : angle 0.83238 ( 8) covalent geometry : bond 0.00371 (16708) covalent geometry : angle 0.53146 (22594) *********************** 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 198 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 168 time to evaluate : 2.541 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: A 627 GLU cc_start: 0.8266 (OUTLIER) cc_final: 0.7910 (mp0) REVERT: A 647 TYR cc_start: 0.8808 (p90) cc_final: 0.8363 (p90) REVERT: A 670 MET cc_start: 0.9392 (mtp) cc_final: 0.9126 (mtm) REVERT: B 674 MET cc_start: 0.8160 (mtm) cc_final: 0.7875 (mtm) REVERT: B 713 GLU cc_start: 0.8685 (tt0) cc_final: 0.8249 (tm-30) REVERT: E 133 LYS cc_start: 0.7358 (mttm) cc_final: 0.6512 (pttp) REVERT: F 22 PHE cc_start: 0.7758 (t80) cc_final: 0.7415 (t80) REVERT: F 65 ARG cc_start: 0.7683 (mtm180) cc_final: 0.6876 (mmt180) REVERT: F 148 TYR cc_start: 0.8296 (t80) cc_final: 0.8088 (t80) REVERT: G 74 ILE cc_start: 0.7971 (pp) cc_final: 0.7739 (mp) REVERT: G 133 LYS cc_start: 0.7578 (mttm) cc_final: 0.6816 (pttp) REVERT: G 136 TRP cc_start: 0.6661 (t-100) cc_final: 0.6390 (m100) REVERT: H 22 PHE cc_start: 0.7804 (t80) cc_final: 0.7511 (t80) REVERT: H 65 ARG cc_start: 0.7745 (mtm180) cc_final: 0.6977 (mmt180) REVERT: H 148 TYR cc_start: 0.8291 (t80) cc_final: 0.7722 (t80) REVERT: C 627 GLU cc_start: 0.8235 (OUTLIER) cc_final: 0.7880 (mp0) REVERT: C 670 MET cc_start: 0.9239 (mtm) cc_final: 0.8975 (mtm) REVERT: D 523 TYR cc_start: 0.7945 (m-80) cc_final: 0.7328 (m-80) REVERT: D 713 GLU cc_start: 0.8775 (tt0) cc_final: 0.8293 (tm-30) outliers start: 30 outliers final: 20 residues processed: 190 average time/residue: 1.5987 time to fit residues: 361.1343 Evaluate side-chains 189 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 167 time to evaluate : 2.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 546 PHE 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 789 LEU Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain E residue 80 ILE Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain F residue 81 MET 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 H residue 14 LEU 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 627 GLU Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain C residue 668 ASP Chi-restraints excluded: chain D residue 474 ILE Chi-restraints excluded: chain D residue 498 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 4 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 149 optimal weight: 4.9990 chunk 104 optimal weight: 10.0000 chunk 177 optimal weight: 1.9990 chunk 134 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 43 optimal weight: 4.9990 chunk 76 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 180 optimal weight: 0.5980 overall best weight: 1.4386 ------------------------------------------------------------------------------- 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 = 0.3821 r_free = 0.3821 target = 0.118466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.092170 restraints weight = 100233.101| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 2.90 r_work: 0.3234 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.4513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.203 16712 Z= 0.210 Angle : 0.755 59.285 22602 Z= 0.423 Chirality : 0.051 1.686 2550 Planarity : 0.004 0.057 2700 Dihedral : 10.561 114.486 2902 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 1.77 % Allowed : 18.35 % Favored : 79.87 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 22.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.20), residues: 1996 helix: 1.78 (0.14), residues: 1256 sheet: -2.07 (0.40), residues: 168 loop : -2.00 (0.27), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP G 136 HIS 0.005 0.001 HIS G 27 PHE 0.104 0.002 PHE A 546 TYR 0.015 0.001 TYR F 142 ARG 0.006 0.000 ARG A 675 Details of bonding type rmsd hydrogen bonds : bond 0.03795 ( 994) hydrogen bonds : angle 3.96253 ( 2904) SS BOND : bond 0.00298 ( 4) SS BOND : angle 0.82185 ( 8) covalent geometry : bond 0.00481 (16708) covalent geometry : angle 0.75477 (22594) ********************** 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: 28 poor density : 167 time to evaluate : 2.540 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: 0.8257 (OUTLIER) cc_final: 0.7900 (mp0) REVERT: A 647 TYR cc_start: 0.8811 (p90) cc_final: 0.8358 (p90) REVERT: A 670 MET cc_start: 0.9391 (mtp) cc_final: 0.9121 (mtm) REVERT: B 674 MET cc_start: 0.8163 (mtm) cc_final: 0.7868 (mtm) REVERT: B 713 GLU cc_start: 0.8686 (tt0) cc_final: 0.8246 (tm-30) REVERT: E 133 LYS cc_start: 0.7356 (mttm) cc_final: 0.6509 (pttp) REVERT: F 22 PHE cc_start: 0.7748 (t80) cc_final: 0.7409 (t80) REVERT: F 65 ARG cc_start: 0.7680 (mtm180) cc_final: 0.6874 (mmt180) REVERT: F 148 TYR cc_start: 0.8284 (t80) cc_final: 0.8058 (t80) REVERT: G 106 PHE cc_start: 0.6467 (OUTLIER) cc_final: 0.5874 (t80) REVERT: G 133 LYS cc_start: 0.7577 (mttm) cc_final: 0.6783 (pttp) REVERT: H 22 PHE cc_start: 0.7799 (t80) cc_final: 0.7507 (t80) REVERT: H 65 ARG cc_start: 0.7742 (mtm180) cc_final: 0.6975 (mmt180) REVERT: H 148 TYR cc_start: 0.8279 (t80) cc_final: 0.7701 (t80) REVERT: C 627 GLU cc_start: 0.8229 (OUTLIER) cc_final: 0.7873 (mp0) REVERT: C 670 MET cc_start: 0.9241 (mtm) cc_final: 0.8978 (mtm) REVERT: D 523 TYR cc_start: 0.7947 (m-80) cc_final: 0.7324 (m-80) REVERT: D 713 GLU cc_start: 0.8778 (tt0) cc_final: 0.8290 (tm-30) outliers start: 28 outliers final: 20 residues processed: 185 average time/residue: 1.6419 time to fit residues: 359.5667 Evaluate side-chains 190 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 167 time to evaluate : 2.473 ------------------------------------------------------------------------------- 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 789 LEU Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain E residue 80 ILE Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain F residue 81 MET 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 H residue 14 LEU 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 600 ILE 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 474 ILE Chi-restraints excluded: chain D residue 498 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 152 optimal weight: 0.7980 chunk 64 optimal weight: 2.9990 chunk 193 optimal weight: 0.9980 chunk 168 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 62 optimal weight: 0.5980 chunk 161 optimal weight: 1.9990 chunk 7 optimal weight: 4.9990 chunk 140 optimal weight: 0.7980 chunk 36 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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 = 0.3820 r_free = 0.3820 target = 0.118434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.092024 restraints weight = 100084.689| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 2.98 r_work: 0.3229 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.4513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.203 16712 Z= 0.210 Angle : 0.755 59.285 22602 Z= 0.423 Chirality : 0.051 1.686 2550 Planarity : 0.004 0.057 2700 Dihedral : 10.561 114.486 2902 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 1.46 % Allowed : 18.67 % Favored : 79.87 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 22.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.20), residues: 1996 helix: 1.78 (0.14), residues: 1256 sheet: -2.07 (0.40), residues: 168 loop : -2.00 (0.27), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP G 136 HIS 0.005 0.001 HIS G 27 PHE 0.104 0.002 PHE A 546 TYR 0.015 0.001 TYR F 142 ARG 0.006 0.000 ARG A 675 Details of bonding type rmsd hydrogen bonds : bond 0.03795 ( 994) hydrogen bonds : angle 3.96253 ( 2904) SS BOND : bond 0.00298 ( 4) SS BOND : angle 0.82185 ( 8) covalent geometry : bond 0.00481 (16708) covalent geometry : angle 0.75477 (22594) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18832.02 seconds wall clock time: 323 minutes 48.67 seconds (19428.67 seconds total)