Starting phenix.real_space_refine on Sat Oct 24 11:59:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zxe_60541/10_2026/8zxe_60541.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zxe_60541/10_2026/8zxe_60541.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8zxe_60541/10_2026/8zxe_60541.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zxe_60541/10_2026/8zxe_60541.map" model { file = "/net/cci-nas-00/data/ceres_data/8zxe_60541/10_2026/8zxe_60541.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zxe_60541/10_2026/8zxe_60541.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.005 sd= 0.132 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: 5 Type Number sf(0) Gaussians P 4 5.49 5 S 62 5.16 5 C 8270 2.51 5 N 2162 2.21 5 O 2522 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13020 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 6163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 763, 6163 Classifications: {'peptide': 763} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 33, 'TRANS': 727} Chain breaks: 2 Chain: "B" Number of atoms: 6163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 763, 6163 Classifications: {'peptide': 763} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 33, 'TRANS': 727} Chain breaks: 2 Chain: "Q" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 65 Unusual residues: {'SRA': 2} Classifications: {'RNA': 1, 'undetermined': 2} Modifications used: {'5*END': 1, 'rna3p': 1} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Chain: "R" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 65 Unusual residues: {'SRA': 2} Classifications: {'RNA': 1, 'undetermined': 2} Modifications used: {'5*END': 1, 'rna3p': 1} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "K" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "L" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 3.08, per 1000 atoms: 0.24 Number of scatterers: 13020 At special positions: 0 Unit cell: (143.175, 100.845, 105.825, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 62 16.00 P 4 15.00 O 2522 8.00 N 2162 7.00 C 8270 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 36 " - pdb=" SG CYS A 51 " distance=2.03 Simple disulfide: pdb=" SG CYS A 98 " - pdb=" SG CYS A 475 " distance=2.03 Simple disulfide: pdb=" SG CYS A 100 " - pdb=" SG CYS A 112 " distance=2.03 Simple disulfide: pdb=" SG CYS A 183 " - pdb=" SG CYS A 189 " distance=2.03 Simple disulfide: pdb=" SG CYS A 260 " - pdb=" SG CYS A 273 " distance=2.03 Simple disulfide: pdb=" SG CYS A 263 " - pdb=" SG CYS A 270 " distance=2.03 Simple disulfide: pdb=" SG CYS A 491 " - pdb=" SG CYS A 521 " distance=2.03 Simple disulfide: pdb=" SG CYS A 787 " - pdb=" SG CYS A 814 " distance=2.03 Simple disulfide: pdb=" SG CYS A 789 " - pdb=" SG CYS A 833 " distance=2.03 Simple disulfide: pdb=" SG CYS B 36 " - pdb=" SG CYS B 51 " distance=2.03 Simple disulfide: pdb=" SG CYS B 98 " - pdb=" SG CYS B 475 " distance=2.03 Simple disulfide: pdb=" SG CYS B 100 " - pdb=" SG CYS B 112 " distance=2.03 Simple disulfide: pdb=" SG CYS B 183 " - pdb=" SG CYS B 189 " distance=2.03 Simple disulfide: pdb=" SG CYS B 260 " - pdb=" SG CYS B 273 " distance=2.03 Simple disulfide: pdb=" SG CYS B 263 " - pdb=" SG CYS B 270 " distance=2.03 Simple disulfide: pdb=" SG CYS B 491 " - pdb=" SG CYS B 521 " distance=2.03 Simple disulfide: pdb=" SG CYS B 787 " - pdb=" SG CYS B 814 " distance=2.03 Simple disulfide: pdb=" SG CYS B 789 " - pdb=" SG CYS B 833 " 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=4, symmetry=0 Links applied ALPHA1-6 " BMA D 3 " - " MAN D 4 " " BMA K 3 " - " MAN K 4 " BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " NAG-ASN " NAG A 901 " - " ASN A 679 " " NAG A 902 " - " ASN A 202 " " NAG A 903 " - " ASN A 720 " " NAG B 901 " - " ASN B 679 " " NAG B 902 " - " ASN B 202 " " NAG B 903 " - " ASN B 720 " " NAG C 1 " - " ASN A 523 " " NAG D 1 " - " ASN A 69 " " NAG E 1 " - " ASN A 215 " " NAG F 1 " - " ASN A 361 " " NAG G 1 " - " ASN A 413 " " NAG H 1 " - " ASN A 534 " " NAG I 1 " - " ASN A 590 " " NAG J 1 " - " ASN B 523 " " NAG K 1 " - " ASN B 69 " " NAG L 1 " - " ASN B 215 " " NAG M 1 " - " ASN B 361 " " NAG N 1 " - " ASN B 413 " " NAG O 1 " - " ASN B 534 " " NAG P 1 " - " ASN B 590 " Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.10 Conformation dependent library (CDL) restraints added in 454.0 milliseconds 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2960 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 12 sheets defined 16.9% alpha, 9.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'A' and resid 81 through 86 removed outlier: 3.623A pdb=" N PHE A 85 " --> pdb=" O PRO A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 169 Processing helix chain 'A' and resid 170 through 172 No H-bonds generated for 'chain 'A' and resid 170 through 172' Processing helix chain 'A' and resid 273 through 277 Processing helix chain 'A' and resid 306 through 311 Processing helix chain 'A' and resid 326 through 333 removed outlier: 3.869A pdb=" N GLY A 331 " --> pdb=" O ALA A 327 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ASP A 332 " --> pdb=" O LYS A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 339 removed outlier: 3.530A pdb=" N HIS A 337 " --> pdb=" O LYS A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 369 Processing helix chain 'A' and resid 386 through 396 Proline residue: A 392 - end of helix removed outlier: 4.187A pdb=" N ASN A 395 " --> pdb=" O PRO A 392 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU A 396 " --> pdb=" O LEU A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 420 removed outlier: 4.032A pdb=" N GLN A 419 " --> pdb=" O MET A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 491 through 495 Processing helix chain 'A' and resid 576 through 582 removed outlier: 3.898A pdb=" N PHE A 580 " --> pdb=" O ASN A 576 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N SER A 582 " --> pdb=" O HIS A 578 " (cutoff:3.500A) Processing helix chain 'A' and resid 590 through 594 removed outlier: 3.834A pdb=" N ASN A 594 " --> pdb=" O PHE A 591 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 635 removed outlier: 4.025A pdb=" N LEU A 634 " --> pdb=" O HIS A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 692 through 697 removed outlier: 3.640A pdb=" N ARG A 696 " --> pdb=" O GLU A 693 " (cutoff:3.500A) Processing helix chain 'A' and resid 717 through 722 Processing helix chain 'A' and resid 763 through 767 Processing helix chain 'A' and resid 768 through 774 removed outlier: 4.177A pdb=" N ASN A 774 " --> pdb=" O ASN A 770 " (cutoff:3.500A) Processing helix chain 'A' and resid 788 through 790 No H-bonds generated for 'chain 'A' and resid 788 through 790' Processing helix chain 'A' and resid 791 through 799 removed outlier: 3.648A pdb=" N GLN A 799 " --> pdb=" O VAL A 795 " (cutoff:3.500A) Processing helix chain 'A' and resid 817 through 821 removed outlier: 3.600A pdb=" N HIS A 820 " --> pdb=" O PRO A 817 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LYS A 821 " --> pdb=" O GLY A 818 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 817 through 821' Processing helix chain 'B' and resid 81 through 86 removed outlier: 3.623A pdb=" N PHE B 85 " --> pdb=" O PRO B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 169 Processing helix chain 'B' and resid 170 through 172 No H-bonds generated for 'chain 'B' and resid 170 through 172' Processing helix chain 'B' and resid 273 through 277 Processing helix chain 'B' and resid 306 through 311 Processing helix chain 'B' and resid 326 through 333 removed outlier: 3.869A pdb=" N GLY B 331 " --> pdb=" O ALA B 327 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ASP B 332 " --> pdb=" O LYS B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 339 removed outlier: 3.530A pdb=" N HIS B 337 " --> pdb=" O LYS B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 363 through 369 Processing helix chain 'B' and resid 386 through 396 Proline residue: B 392 - end of helix removed outlier: 4.186A pdb=" N ASN B 395 " --> pdb=" O PRO B 392 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU B 396 " --> pdb=" O LEU B 393 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 420 removed outlier: 4.033A pdb=" N GLN B 419 " --> pdb=" O MET B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 491 through 495 Processing helix chain 'B' and resid 576 through 582 removed outlier: 3.898A pdb=" N PHE B 580 " --> pdb=" O ASN B 576 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N SER B 582 " --> pdb=" O HIS B 578 " (cutoff:3.500A) Processing helix chain 'B' and resid 590 through 594 removed outlier: 3.833A pdb=" N ASN B 594 " --> pdb=" O PHE B 591 " (cutoff:3.500A) Processing helix chain 'B' and resid 630 through 635 removed outlier: 4.024A pdb=" N LEU B 634 " --> pdb=" O HIS B 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 692 through 697 removed outlier: 3.641A pdb=" N ARG B 696 " --> pdb=" O GLU B 693 " (cutoff:3.500A) Processing helix chain 'B' and resid 717 through 722 Processing helix chain 'B' and resid 763 through 767 Processing helix chain 'B' and resid 768 through 774 removed outlier: 4.176A pdb=" N ASN B 774 " --> pdb=" O ASN B 770 " (cutoff:3.500A) Processing helix chain 'B' and resid 788 through 790 No H-bonds generated for 'chain 'B' and resid 788 through 790' Processing helix chain 'B' and resid 791 through 799 removed outlier: 3.648A pdb=" N GLN B 799 " --> pdb=" O VAL B 795 " (cutoff:3.500A) Processing helix chain 'B' and resid 817 through 821 removed outlier: 3.599A pdb=" N HIS B 820 " --> pdb=" O PRO B 817 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS B 821 " --> pdb=" O GLY B 818 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 817 through 821' Processing sheet with id=AA1, first strand: chain 'A' and resid 37 through 41 removed outlier: 6.542A pdb=" N VAL A 47 " --> pdb=" O ASN A 69 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N THR A 71 " --> pdb=" O VAL A 47 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N VAL A 49 " --> pdb=" O THR A 71 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ILE A 94 " --> pdb=" O TYR A 133 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N LEU A 132 " --> pdb=" O SER A 154 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N LEU A 153 " --> pdb=" O TYR A 178 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N LEU A 375 " --> pdb=" O ASP A 403 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N LEU A 402 " --> pdb=" O ASP A 427 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N LEU A 498 " --> pdb=" O ASN A 523 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N LEU A 522 " --> pdb=" O ASP A 548 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N LEU A 571 " --> pdb=" O MET A 602 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N LEU A 601 " --> pdb=" O GLU A 625 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 79 through 80 Processing sheet with id=AA3, first strand: chain 'A' and resid 162 through 163 Processing sheet with id=AA4, first strand: chain 'A' and resid 357 through 359 removed outlier: 6.632A pdb=" N ALA A 358 " --> pdb=" O GLU A 384 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE A 411 " --> pdb=" O LYS A 383 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 530 through 531 Processing sheet with id=AA6, first strand: chain 'A' and resid 727 through 729 Processing sheet with id=AA7, first strand: chain 'B' and resid 37 through 41 removed outlier: 6.543A pdb=" N VAL B 47 " --> pdb=" O ASN B 69 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N THR B 71 " --> pdb=" O VAL B 47 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N VAL B 49 " --> pdb=" O THR B 71 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ILE B 94 " --> pdb=" O TYR B 133 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N LEU B 132 " --> pdb=" O SER B 154 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N LEU B 153 " --> pdb=" O TYR B 178 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N LEU B 375 " --> pdb=" O ASP B 403 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N LEU B 402 " --> pdb=" O ASP B 427 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N LEU B 498 " --> pdb=" O ASN B 523 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N LEU B 522 " --> pdb=" O ASP B 548 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N LEU B 571 " --> pdb=" O MET B 602 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N LEU B 601 " --> pdb=" O GLU B 625 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 79 through 80 Processing sheet with id=AA9, first strand: chain 'B' and resid 162 through 163 Processing sheet with id=AB1, first strand: chain 'B' and resid 357 through 359 removed outlier: 6.632A pdb=" N ALA B 358 " --> pdb=" O GLU B 384 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE B 411 " --> pdb=" O LYS B 383 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 530 through 531 Processing sheet with id=AB3, first strand: chain 'B' and resid 727 through 729 154 hydrogen bonds defined for protein. 294 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: 2.24 Time building geometry restraints manager: 1.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.37: 4178 1.37 - 1.54: 8959 1.54 - 1.71: 69 1.71 - 1.89: 78 1.89 - 2.06: 4 Bond restraints: 13288 Sorted by residual: bond pdb=" P SRA Q 3 " pdb=" S2P SRA Q 3 " ideal model delta sigma weight residual 1.921 2.059 -0.138 2.00e-02 2.50e+03 4.74e+01 bond pdb=" P SRA R 3 " pdb=" S2P SRA R 3 " ideal model delta sigma weight residual 1.921 2.058 -0.137 2.00e-02 2.50e+03 4.69e+01 bond pdb=" P SRA Q 2 " pdb=" OP1 SRA Q 2 " ideal model delta sigma weight residual 1.593 1.461 0.132 2.00e-02 2.50e+03 4.39e+01 bond pdb=" P SRA R 2 " pdb=" OP1 SRA R 2 " ideal model delta sigma weight residual 1.593 1.461 0.132 2.00e-02 2.50e+03 4.33e+01 bond pdb=" P SRA Q 3 " pdb=" OP1 SRA Q 3 " ideal model delta sigma weight residual 1.593 1.468 0.125 2.00e-02 2.50e+03 3.93e+01 ... (remaining 13283 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.06: 17602 2.06 - 4.11: 317 4.11 - 6.17: 69 6.17 - 8.22: 28 8.22 - 10.28: 8 Bond angle restraints: 18024 Sorted by residual: angle pdb=" C CYS A 270 " pdb=" N THR A 271 " pdb=" CA THR A 271 " ideal model delta sigma weight residual 122.65 115.62 7.03 1.66e+00 3.63e-01 1.79e+01 angle pdb=" CA CYS A 273 " pdb=" C CYS A 273 " pdb=" O CYS A 273 " ideal model delta sigma weight residual 122.01 117.62 4.39 1.05e+00 9.07e-01 1.75e+01 angle pdb=" CA CYS B 273 " pdb=" C CYS B 273 " pdb=" O CYS B 273 " ideal model delta sigma weight residual 122.01 117.66 4.35 1.05e+00 9.07e-01 1.71e+01 angle pdb=" C CYS B 270 " pdb=" N THR B 271 " pdb=" CA THR B 271 " ideal model delta sigma weight residual 122.65 115.97 6.68 1.66e+00 3.63e-01 1.62e+01 angle pdb=" C3' OMG Q 1 " pdb=" C2' OMG Q 1 " pdb=" C1' OMG Q 1 " ideal model delta sigma weight residual 101.30 104.92 -3.62 1.00e+00 1.00e+00 1.31e+01 ... (remaining 18019 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.75: 7819 21.75 - 43.50: 652 43.50 - 65.25: 139 65.25 - 87.00: 58 87.00 - 108.75: 26 Dihedral angle restraints: 8694 sinusoidal: 4170 harmonic: 4524 Sorted by residual: dihedral pdb=" CB CYS B 789 " pdb=" SG CYS B 789 " pdb=" SG CYS B 833 " pdb=" CB CYS B 833 " ideal model delta sinusoidal sigma weight residual -86.00 -171.61 85.61 1 1.00e+01 1.00e-02 8.87e+01 dihedral pdb=" CB CYS A 789 " pdb=" SG CYS A 789 " pdb=" SG CYS A 833 " pdb=" CB CYS A 833 " ideal model delta sinusoidal sigma weight residual -86.00 -171.57 85.57 1 1.00e+01 1.00e-02 8.86e+01 dihedral pdb=" CB CYS B 263 " pdb=" SG CYS B 263 " pdb=" SG CYS B 270 " pdb=" CB CYS B 270 " ideal model delta sinusoidal sigma weight residual 93.00 175.31 -82.31 1 1.00e+01 1.00e-02 8.32e+01 ... (remaining 8691 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 1845 0.056 - 0.111: 276 0.111 - 0.167: 65 0.167 - 0.223: 4 0.223 - 0.278: 8 Chirality restraints: 2198 Sorted by residual: chirality pdb=" C5 BMA L 3 " pdb=" C4 BMA L 3 " pdb=" C6 BMA L 3 " pdb=" O5 BMA L 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.28 2.00e-01 2.50e+01 1.94e+00 chirality pdb=" C5 BMA E 3 " pdb=" C4 BMA E 3 " pdb=" C6 BMA E 3 " pdb=" O5 BMA E 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.86e+00 chirality pdb=" C5 BMA K 3 " pdb=" C4 BMA K 3 " pdb=" C6 BMA K 3 " pdb=" O5 BMA K 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.86e+00 ... (remaining 2195 not shown) Planarity restraints: 2236 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA CYS B 270 " -0.014 2.00e-02 2.50e+03 2.68e-02 7.21e+00 pdb=" C CYS B 270 " 0.046 2.00e-02 2.50e+03 pdb=" O CYS B 270 " -0.017 2.00e-02 2.50e+03 pdb=" N THR B 271 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS A 270 " -0.013 2.00e-02 2.50e+03 2.55e-02 6.48e+00 pdb=" C CYS A 270 " 0.044 2.00e-02 2.50e+03 pdb=" O CYS A 270 " -0.016 2.00e-02 2.50e+03 pdb=" N THR A 271 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 322 " 0.009 2.00e-02 2.50e+03 1.71e-02 2.92e+00 pdb=" C SER A 322 " -0.030 2.00e-02 2.50e+03 pdb=" O SER A 322 " 0.011 2.00e-02 2.50e+03 pdb=" N GLN A 323 " 0.010 2.00e-02 2.50e+03 ... (remaining 2233 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 3198 2.79 - 3.32: 11268 3.32 - 3.85: 21552 3.85 - 4.37: 25752 4.37 - 4.90: 43572 Nonbonded interactions: 105342 Sorted by model distance: nonbonded pdb=" OG1 THR A 788 " pdb=" OD1 ASP A 790 " model vdw 2.269 3.040 nonbonded pdb=" OG1 THR B 788 " pdb=" OD1 ASP B 790 " model vdw 2.269 3.040 nonbonded pdb=" OD1 ASP A 572 " pdb=" OG SER A 574 " model vdw 2.319 3.040 nonbonded pdb=" OD1 ASP B 572 " pdb=" OG SER B 574 " model vdw 2.320 3.040 nonbonded pdb=" O LYS B 119 " pdb=" OG SER B 122 " model vdw 2.336 3.040 ... (remaining 105337 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'E' selection = chain 'J' selection = chain 'L' } ncs_group { reference = chain 'D' selection = chain 'K' } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' } ncs_group { reference = chain 'Q' selection = chain 'R' } 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: 0.590 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: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 12.430 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.030 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:6.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 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 : 0.006 0.138 13352 Z= 0.304 Angle : 0.725 10.280 18186 Z= 0.335 Chirality : 0.047 0.278 2198 Planarity : 0.003 0.042 2216 Dihedral : 18.137 108.747 5680 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.40 % Allowed : 4.76 % Favored : 94.85 % Rotamer: Outliers : 0.70 % Allowed : 21.17 % Favored : 78.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.79 (0.23), residues: 1514 helix: -2.99 (0.36), residues: 142 sheet: -1.27 (0.36), residues: 280 loop : 0.14 (0.20), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 164 TYR 0.009 0.001 TYR B 184 PHE 0.010 0.001 PHE A 506 TRP 0.003 0.000 TRP B 692 HIS 0.002 0.000 HIS B 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00570 / 0.30 (13288) covalent geometry : angle 0.72081 / 0.33 (18024) SS BOND : bond 0.00157 / 0.13 ( 18) SS BOND : angle 0.81539 / 0.62 ( 36) hydrogen bonds : bond 0.32510 / 20.60 ( 154) hydrogen bonds : angle 6.63287 / 4.54 ( 294) Misc. bond : bond 0.03366 / 1.59 ( 4) link_ALPHA1-6 : bond 0.00309 / 0.16 ( 2) link_ALPHA1-6 : angle 1.54503 / 0.87 ( 6) link_BETA1-4 : bond 0.00430 / 0.30 ( 20) link_BETA1-4 : angle 1.18308 / 0.86 ( 60) link_NAG-ASN : bond 0.00169 / 0.11 ( 20) link_NAG-ASN : angle 1.04181 / 0.76 ( 60) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 152 time to evaluate : 0.527 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 119 LYS cc_start: 0.9143 (mmmt) cc_final: 0.8929 (mmtm) REVERT: A 246 ASN cc_start: 0.9026 (t0) cc_final: 0.8774 (m110) REVERT: A 291 GLU cc_start: 0.8371 (mp0) cc_final: 0.7724 (mp0) REVERT: A 619 GLU cc_start: 0.8719 (mm-30) cc_final: 0.8489 (pm20) REVERT: A 648 ASN cc_start: 0.8596 (m-40) cc_final: 0.8348 (m-40) REVERT: A 785 PHE cc_start: 0.7165 (m-80) cc_final: 0.6766 (m-80) REVERT: A 795 VAL cc_start: 0.8054 (t) cc_final: 0.7723 (m) REVERT: B 276 ASN cc_start: 0.9002 (m-40) cc_final: 0.8503 (p0) REVERT: B 291 GLU cc_start: 0.8399 (mp0) cc_final: 0.7984 (mp0) REVERT: B 603 MET cc_start: 0.9091 (ptm) cc_final: 0.8854 (ptm) REVERT: B 654 GLU cc_start: 0.8446 (tt0) cc_final: 0.7748 (mt-10) REVERT: B 690 PHE cc_start: 0.8464 (t80) cc_final: 0.8155 (t80) REVERT: B 785 PHE cc_start: 0.7333 (m-80) cc_final: 0.6770 (m-80) REVERT: B 795 VAL cc_start: 0.7973 (t) cc_final: 0.7736 (m) outliers start: 10 outliers final: 9 residues processed: 162 average time/residue: 0.6096 time to fit residues: 107.4627 Evaluate side-chains 81 residues out of total 1436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 72 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 112 CYS Chi-restraints excluded: chain A residue 352 GLU Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 812 VAL Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 112 CYS Chi-restraints excluded: chain B residue 352 GLU Chi-restraints excluded: chain B residue 812 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: [98, 107, 10, 66, 130, 124, 103, 77, 122, 91, 149] chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 6.9990 chunk 149 optimal weight: 0.1980 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 137 ASN B 137 ASN B 246 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.096669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.066763 restraints weight = 24477.776| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 3.18 r_work: 0.2884 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.1655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 13352 Z= 0.148 Angle : 0.580 8.798 18186 Z= 0.284 Chirality : 0.044 0.198 2198 Planarity : 0.004 0.048 2216 Dihedral : 10.644 68.769 2603 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.89 % Favored : 94.85 % Rotamer: Outliers : 1.88 % Allowed : 21.66 % Favored : 76.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.80 (0.23), residues: 1514 helix: -3.06 (0.33), residues: 150 sheet: -1.49 (0.34), residues: 280 loop : 0.24 (0.21), residues: 1084 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 121 TYR 0.015 0.001 TYR A 751 PHE 0.013 0.001 PHE A 506 TRP 0.011 0.001 TRP A 796 HIS 0.003 0.001 HIS A 781 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.15 (13288) covalent geometry : angle 0.56776 / 0.28 (18024) SS BOND : bond 0.00367 / 0.28 ( 18) SS BOND : angle 0.58166 / 0.42 ( 36) hydrogen bonds : bond 0.04999 / 3.19 ( 154) hydrogen bonds : angle 5.56026 / 3.82 ( 294) Misc. bond : bond 0.00130 / 0.06 ( 4) link_ALPHA1-6 : bond 0.00552 / 0.28 ( 2) link_ALPHA1-6 : angle 1.74417 / 0.90 ( 6) link_BETA1-4 : bond 0.00495 / 0.34 ( 20) link_BETA1-4 : angle 1.81168 / 1.30 ( 60) link_NAG-ASN : bond 0.00187 / 0.11 ( 20) link_NAG-ASN : angle 1.15247 / 0.84 ( 60) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 79 time to evaluate : 0.495 Fit side-chains REVERT: A 96 PHE cc_start: 0.8676 (OUTLIER) cc_final: 0.7837 (t80) REVERT: A 119 LYS cc_start: 0.9127 (mmmt) cc_final: 0.8927 (mmtm) REVERT: A 242 GLU cc_start: 0.8784 (pm20) cc_final: 0.8397 (pm20) REVERT: A 246 ASN cc_start: 0.9247 (t0) cc_final: 0.8784 (m110) REVERT: A 291 GLU cc_start: 0.8686 (OUTLIER) cc_final: 0.8019 (mp0) REVERT: A 352 GLU cc_start: 0.9068 (OUTLIER) cc_final: 0.8793 (mt-10) REVERT: A 619 GLU cc_start: 0.9018 (mm-30) cc_final: 0.8584 (pm20) REVERT: A 654 GLU cc_start: 0.8165 (tt0) cc_final: 0.7468 (mt-10) REVERT: A 796 TRP cc_start: 0.8384 (t60) cc_final: 0.7930 (t-100) REVERT: B 96 PHE cc_start: 0.8649 (OUTLIER) cc_final: 0.8275 (t80) REVERT: B 246 ASN cc_start: 0.9197 (OUTLIER) cc_final: 0.8826 (m110) REVERT: B 291 GLU cc_start: 0.8695 (OUTLIER) cc_final: 0.8215 (mp0) REVERT: B 352 GLU cc_start: 0.9053 (OUTLIER) cc_final: 0.8743 (mt-10) REVERT: B 619 GLU cc_start: 0.8990 (mm-30) cc_final: 0.8606 (mp0) REVERT: B 654 GLU cc_start: 0.8170 (tt0) cc_final: 0.7545 (mt-10) REVERT: B 690 PHE cc_start: 0.8283 (t80) cc_final: 0.7918 (t80) REVERT: B 796 TRP cc_start: 0.8256 (t60) cc_final: 0.7834 (t-100) outliers start: 27 outliers final: 5 residues processed: 94 average time/residue: 0.5607 time to fit residues: 57.9622 Evaluate side-chains 77 residues out of total 1436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 65 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 PHE Chi-restraints excluded: chain A residue 291 GLU Chi-restraints excluded: chain A residue 352 GLU Chi-restraints excluded: chain A residue 602 MET Chi-restraints excluded: chain A residue 812 VAL Chi-restraints excluded: chain B residue 96 PHE Chi-restraints excluded: chain B residue 236 MET Chi-restraints excluded: chain B residue 246 ASN Chi-restraints excluded: chain B residue 291 GLU Chi-restraints excluded: chain B residue 352 GLU Chi-restraints excluded: chain B residue 550 SER Chi-restraints excluded: chain B residue 812 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: [26, 42, 58, 5, 127, 121, 137, 94, 89, 129, 149] chunk 26 optimal weight: 4.9990 chunk 42 optimal weight: 0.7980 chunk 58 optimal weight: 5.9990 chunk 5 optimal weight: 10.0000 chunk 127 optimal weight: 3.9990 chunk 121 optimal weight: 4.9990 chunk 137 optimal weight: 0.0040 chunk 94 optimal weight: 7.9990 chunk 89 optimal weight: 4.9990 chunk 129 optimal weight: 4.9990 chunk 149 optimal weight: 7.9990 overall best weight: 2.9598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 300 ASN ** B 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 300 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.091373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.061171 restraints weight = 24732.133| |-----------------------------------------------------------------------------| r_work (start): 0.2924 rms_B_bonded: 3.20 r_work: 0.2765 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.2506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 13352 Z= 0.263 Angle : 0.633 8.602 18186 Z= 0.311 Chirality : 0.047 0.197 2198 Planarity : 0.004 0.061 2216 Dihedral : 7.394 54.345 2598 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.61 % Favored : 93.13 % Rotamer: Outliers : 2.58 % Allowed : 21.59 % Favored : 75.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.16 (0.22), residues: 1514 helix: -3.03 (0.31), residues: 170 sheet: -1.73 (0.33), residues: 280 loop : 0.00 (0.20), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 121 TYR 0.012 0.002 TYR A 133 PHE 0.017 0.002 PHE B 794 TRP 0.012 0.002 TRP A 797 HIS 0.003 0.001 HIS B 781 Details of bonding type rmsd/Z covalent geometry : bond 0.00620 / 0.26 (13288) covalent geometry : angle 0.62033 / 0.31 (18024) SS BOND : bond 0.00506 / 0.38 ( 18) SS BOND : angle 0.52896 / 0.35 ( 36) hydrogen bonds : bond 0.05009 / 3.22 ( 154) hydrogen bonds : angle 5.45076 / 3.76 ( 294) Misc. bond : bond 0.00130 / 0.05 ( 4) link_ALPHA1-6 : bond 0.00951 / 0.48 ( 2) link_ALPHA1-6 : angle 1.42659 / 0.67 ( 6) link_BETA1-4 : bond 0.00394 / 0.26 ( 20) link_BETA1-4 : angle 1.89982 / 1.31 ( 60) link_NAG-ASN : bond 0.00479 / 0.32 ( 20) link_NAG-ASN : angle 1.37576 / 0.96 ( 60) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 70 time to evaluate : 0.502 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 242 GLU cc_start: 0.8834 (pm20) cc_final: 0.8627 (pm20) REVERT: A 291 GLU cc_start: 0.8789 (OUTLIER) cc_final: 0.8174 (mp0) REVERT: A 619 GLU cc_start: 0.9064 (mm-30) cc_final: 0.8659 (mp0) REVERT: A 654 GLU cc_start: 0.8285 (tt0) cc_final: 0.7620 (mt-10) REVERT: A 824 SER cc_start: 0.8828 (m) cc_final: 0.8351 (t) REVERT: B 96 PHE cc_start: 0.8854 (OUTLIER) cc_final: 0.8295 (t80) REVERT: B 242 GLU cc_start: 0.8911 (mt-10) cc_final: 0.8524 (mt-10) REVERT: B 246 ASN cc_start: 0.9171 (m-40) cc_final: 0.8891 (m110) REVERT: B 291 GLU cc_start: 0.8728 (mp0) cc_final: 0.8231 (mp0) REVERT: B 619 GLU cc_start: 0.9028 (mm-30) cc_final: 0.8627 (mp0) REVERT: B 654 GLU cc_start: 0.8282 (tt0) cc_final: 0.7621 (mt-10) REVERT: B 797 TRP cc_start: 0.8099 (t60) cc_final: 0.7898 (t60) outliers start: 37 outliers final: 14 residues processed: 100 average time/residue: 0.5617 time to fit residues: 62.0536 Evaluate side-chains 79 residues out of total 1436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 63 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 291 GLU Chi-restraints excluded: chain A residue 352 GLU Chi-restraints excluded: chain A residue 429 SER Chi-restraints excluded: chain A residue 491 CYS Chi-restraints excluded: chain A residue 550 SER Chi-restraints excluded: chain A residue 602 MET Chi-restraints excluded: chain A residue 756 SER Chi-restraints excluded: chain A residue 774 ASN Chi-restraints excluded: chain A residue 812 VAL Chi-restraints excluded: chain B residue 96 PHE Chi-restraints excluded: chain B residue 352 GLU Chi-restraints excluded: chain B residue 429 SER Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 756 SER Chi-restraints excluded: chain B residue 812 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: [103, 44, 88, 35, 36, 77, 126, 125, 30, 49, 38] chunk 103 optimal weight: 0.6980 chunk 44 optimal weight: 1.9990 chunk 88 optimal weight: 6.9990 chunk 35 optimal weight: 0.0980 chunk 36 optimal weight: 0.8980 chunk 77 optimal weight: 10.0000 chunk 126 optimal weight: 0.8980 chunk 125 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 246 ASN A 710 GLN ** B 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 710 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.093658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.063718 restraints weight = 24484.460| |-----------------------------------------------------------------------------| r_work (start): 0.2968 rms_B_bonded: 3.17 r_work: 0.2809 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.2526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 13352 Z= 0.100 Angle : 0.526 8.969 18186 Z= 0.263 Chirality : 0.042 0.150 2198 Planarity : 0.003 0.067 2216 Dihedral : 6.078 53.519 2598 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.62 % Favored : 95.11 % Rotamer: Outliers : 2.44 % Allowed : 21.66 % Favored : 75.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.98 (0.23), residues: 1514 helix: -2.88 (0.34), residues: 162 sheet: -1.73 (0.33), residues: 280 loop : 0.13 (0.20), residues: 1072 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B 121 TYR 0.009 0.001 TYR A 546 PHE 0.023 0.001 PHE A 785 TRP 0.008 0.001 TRP B 797 HIS 0.003 0.001 HIS B 781 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.10 (13288) covalent geometry : angle 0.51583 / 0.26 (18024) SS BOND : bond 0.00195 / 0.14 ( 18) SS BOND : angle 0.42625 / 0.28 ( 36) hydrogen bonds : bond 0.03381 / 2.19 ( 154) hydrogen bonds : angle 5.17682 / 3.54 ( 294) Misc. bond : bond 0.00049 / 0.02 ( 4) link_ALPHA1-6 : bond 0.00777 / 0.39 ( 2) link_ALPHA1-6 : angle 1.43424 / 0.72 ( 6) link_BETA1-4 : bond 0.00463 / 0.32 ( 20) link_BETA1-4 : angle 1.54474 / 1.09 ( 60) link_NAG-ASN : bond 0.00168 / 0.10 ( 20) link_NAG-ASN : angle 1.05063 / 0.76 ( 60) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 66 time to evaluate : 0.440 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 96 PHE cc_start: 0.8899 (OUTLIER) cc_final: 0.8075 (t80) REVERT: A 242 GLU cc_start: 0.8810 (pm20) cc_final: 0.8491 (pm20) REVERT: A 246 ASN cc_start: 0.9153 (OUTLIER) cc_final: 0.8687 (m110) REVERT: A 291 GLU cc_start: 0.8784 (mp0) cc_final: 0.8170 (mp0) REVERT: A 619 GLU cc_start: 0.9033 (mm-30) cc_final: 0.8678 (mp0) REVERT: A 654 GLU cc_start: 0.8318 (tt0) cc_final: 0.7663 (mt-10) REVERT: A 684 LYS cc_start: 0.8079 (OUTLIER) cc_final: 0.7782 (mtmm) REVERT: A 824 SER cc_start: 0.8851 (m) cc_final: 0.8374 (t) REVERT: B 40 LEU cc_start: 0.8281 (tp) cc_final: 0.7915 (tm) REVERT: B 246 ASN cc_start: 0.9059 (m-40) cc_final: 0.8741 (m110) REVERT: B 291 GLU cc_start: 0.8797 (OUTLIER) cc_final: 0.8284 (mp0) REVERT: B 339 LEU cc_start: 0.9252 (OUTLIER) cc_final: 0.8933 (mt) REVERT: B 619 GLU cc_start: 0.8988 (mm-30) cc_final: 0.8662 (mp0) REVERT: B 654 GLU cc_start: 0.8326 (tt0) cc_final: 0.7676 (mt-10) REVERT: B 684 LYS cc_start: 0.8153 (OUTLIER) cc_final: 0.7844 (mtmm) REVERT: B 797 TRP cc_start: 0.8152 (t60) cc_final: 0.7938 (t60) REVERT: B 824 SER cc_start: 0.8835 (m) cc_final: 0.8299 (t) outliers start: 35 outliers final: 13 residues processed: 93 average time/residue: 0.5477 time to fit residues: 56.2874 Evaluate side-chains 83 residues out of total 1436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 64 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 PHE Chi-restraints excluded: chain A residue 236 MET Chi-restraints excluded: chain A residue 246 ASN Chi-restraints excluded: chain A residue 352 GLU Chi-restraints excluded: chain A residue 429 SER Chi-restraints excluded: chain A residue 684 LYS Chi-restraints excluded: chain A residue 756 SER Chi-restraints excluded: chain A residue 812 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 236 MET Chi-restraints excluded: chain B residue 291 GLU Chi-restraints excluded: chain B residue 339 LEU Chi-restraints excluded: chain B residue 352 GLU Chi-restraints excluded: chain B residue 429 SER Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 491 CYS Chi-restraints excluded: chain B residue 602 MET Chi-restraints excluded: chain B residue 684 LYS Chi-restraints excluded: chain B residue 812 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: [141, 144, 81, 146, 110, 50, 0, 104, 63, 94, 36] chunk 141 optimal weight: 9.9990 chunk 144 optimal weight: 3.9990 chunk 81 optimal weight: 0.8980 chunk 146 optimal weight: 2.9990 chunk 110 optimal weight: 4.9990 chunk 50 optimal weight: 5.9990 chunk 0 optimal weight: 9.9990 chunk 104 optimal weight: 5.9990 chunk 63 optimal weight: 8.9990 chunk 94 optimal weight: 4.9990 chunk 36 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 50.5413 > 50:) overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 246 ASN ** B 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.089325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.059288 restraints weight = 25064.695| |-----------------------------------------------------------------------------| r_work (start): 0.2871 rms_B_bonded: 3.19 r_work: 0.2711 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.3089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.059 13352 Z= 0.311 Angle : 0.643 8.961 18186 Z= 0.321 Chirality : 0.048 0.205 2198 Planarity : 0.004 0.056 2216 Dihedral : 6.246 59.628 2598 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.40 % Allowed : 6.74 % Favored : 92.87 % Rotamer: Outliers : 3.62 % Allowed : 20.33 % Favored : 76.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.11 (0.22), residues: 1514 helix: -2.84 (0.34), residues: 158 sheet: -1.90 (0.32), residues: 280 loop : 0.03 (0.20), residues: 1076 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 121 TYR 0.013 0.002 TYR B 133 PHE 0.018 0.002 PHE B 506 TRP 0.013 0.001 TRP A 793 HIS 0.003 0.001 HIS A 298 Details of bonding type rmsd/Z covalent geometry : bond 0.00739 / 0.31 (13288) covalent geometry : angle 0.63155 / 0.32 (18024) SS BOND : bond 0.00512 / 0.38 ( 18) SS BOND : angle 0.52675 / 0.36 ( 36) hydrogen bonds : bond 0.04734 / 3.07 ( 154) hydrogen bonds : angle 5.36631 / 3.68 ( 294) Misc. bond : bond 0.00077 / 0.03 ( 4) link_ALPHA1-6 : bond 0.00879 / 0.44 ( 2) link_ALPHA1-6 : angle 1.26778 / 0.58 ( 6) link_BETA1-4 : bond 0.00425 / 0.27 ( 20) link_BETA1-4 : angle 1.69723 / 1.11 ( 60) link_NAG-ASN : bond 0.00579 / 0.40 ( 20) link_NAG-ASN : angle 1.52701 / 1.04 ( 60) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 62 time to evaluate : 0.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 PHE cc_start: 0.8972 (OUTLIER) cc_final: 0.8098 (t80) REVERT: A 242 GLU cc_start: 0.8883 (pm20) cc_final: 0.8672 (pm20) REVERT: A 291 GLU cc_start: 0.8771 (OUTLIER) cc_final: 0.8241 (mp0) REVERT: A 517 SER cc_start: 0.9125 (OUTLIER) cc_final: 0.8812 (p) REVERT: A 550 SER cc_start: 0.9002 (OUTLIER) cc_final: 0.8789 (p) REVERT: A 619 GLU cc_start: 0.9095 (mm-30) cc_final: 0.8632 (mp0) REVERT: A 684 LYS cc_start: 0.7931 (OUTLIER) cc_final: 0.7700 (mtmm) REVERT: A 824 SER cc_start: 0.8755 (m) cc_final: 0.8286 (t) REVERT: B 40 LEU cc_start: 0.8437 (tp) cc_final: 0.8062 (tm) REVERT: B 121 ARG cc_start: 0.9202 (mtm-85) cc_final: 0.8909 (mtm-85) REVERT: B 291 GLU cc_start: 0.8806 (OUTLIER) cc_final: 0.8304 (mp0) REVERT: B 339 LEU cc_start: 0.9306 (OUTLIER) cc_final: 0.9037 (mt) REVERT: B 517 SER cc_start: 0.9135 (OUTLIER) cc_final: 0.8799 (p) REVERT: B 550 SER cc_start: 0.9008 (OUTLIER) cc_final: 0.8784 (p) REVERT: B 684 LYS cc_start: 0.8010 (OUTLIER) cc_final: 0.7783 (mtmm) REVERT: B 797 TRP cc_start: 0.8308 (t60) cc_final: 0.7959 (t60) REVERT: B 824 SER cc_start: 0.8734 (m) cc_final: 0.8240 (t) outliers start: 52 outliers final: 19 residues processed: 102 average time/residue: 0.5043 time to fit residues: 57.1521 Evaluate side-chains 84 residues out of total 1436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 55 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 96 PHE Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 236 MET Chi-restraints excluded: chain A residue 291 GLU Chi-restraints excluded: chain A residue 352 GLU Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 429 SER Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 491 CYS Chi-restraints excluded: chain A residue 517 SER Chi-restraints excluded: chain A residue 550 SER Chi-restraints excluded: chain A residue 684 LYS Chi-restraints excluded: chain A residue 756 SER Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 812 VAL Chi-restraints excluded: chain B residue 236 MET Chi-restraints excluded: chain B residue 291 GLU Chi-restraints excluded: chain B residue 339 LEU Chi-restraints excluded: chain B residue 352 GLU Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 491 CYS Chi-restraints excluded: chain B residue 517 SER Chi-restraints excluded: chain B residue 550 SER Chi-restraints excluded: chain B residue 684 LYS Chi-restraints excluded: chain B residue 756 SER Chi-restraints excluded: chain B residue 780 LEU Chi-restraints excluded: chain B residue 812 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: [149, 150, 63, 57, 1, 151, 90, 59, 98, 84, 18] chunk 149 optimal weight: 8.9990 chunk 150 optimal weight: 0.9990 chunk 63 optimal weight: 5.9990 chunk 57 optimal weight: 4.9990 chunk 1 optimal weight: 10.0000 chunk 151 optimal weight: 4.9990 chunk 90 optimal weight: 4.9990 chunk 59 optimal weight: 0.9980 chunk 98 optimal weight: 0.0470 chunk 84 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 overall best weight: 1.8084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 246 ASN ** B 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.090835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.060951 restraints weight = 24336.820| |-----------------------------------------------------------------------------| r_work (start): 0.2901 rms_B_bonded: 3.19 r_work: 0.2741 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.3122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 13352 Z= 0.167 Angle : 0.547 9.305 18186 Z= 0.277 Chirality : 0.044 0.156 2198 Planarity : 0.003 0.036 2216 Dihedral : 6.068 58.562 2598 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.40 % Allowed : 5.02 % Favored : 94.58 % Rotamer: Outliers : 2.65 % Allowed : 21.45 % Favored : 75.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.11 (0.23), residues: 1514 helix: -2.96 (0.33), residues: 162 sheet: -1.94 (0.32), residues: 280 loop : 0.08 (0.20), residues: 1072 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 121 TYR 0.010 0.001 TYR B 546 PHE 0.020 0.001 PHE A 785 TRP 0.009 0.001 TRP A 793 HIS 0.003 0.001 HIS B 781 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.17 (13288) covalent geometry : angle 0.53842 / 0.28 (18024) SS BOND : bond 0.00324 / 0.24 ( 18) SS BOND : angle 0.44591 / 0.29 ( 36) hydrogen bonds : bond 0.03700 / 2.42 ( 154) hydrogen bonds : angle 5.21475 / 3.57 ( 294) Misc. bond : bond 0.00025 / 0.01 ( 4) link_ALPHA1-6 : bond 0.00813 / 0.41 ( 2) link_ALPHA1-6 : angle 1.31542 / 0.66 ( 6) link_BETA1-4 : bond 0.00426 / 0.29 ( 20) link_BETA1-4 : angle 1.38581 / 0.94 ( 60) link_NAG-ASN : bond 0.00268 / 0.18 ( 20) link_NAG-ASN : angle 1.20190 / 0.85 ( 60) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 63 time to evaluate : 0.333 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 96 PHE cc_start: 0.8952 (OUTLIER) cc_final: 0.8140 (t80) REVERT: A 242 GLU cc_start: 0.8885 (pm20) cc_final: 0.8682 (pm20) REVERT: A 291 GLU cc_start: 0.8765 (OUTLIER) cc_final: 0.8238 (mp0) REVERT: A 619 GLU cc_start: 0.9070 (mm-30) cc_final: 0.8620 (mp0) REVERT: A 684 LYS cc_start: 0.7914 (OUTLIER) cc_final: 0.7678 (mtmm) REVERT: A 824 SER cc_start: 0.8787 (m) cc_final: 0.8341 (t) REVERT: B 40 LEU cc_start: 0.8422 (tp) cc_final: 0.8041 (tm) REVERT: B 96 PHE cc_start: 0.8928 (OUTLIER) cc_final: 0.8365 (t80) REVERT: B 121 ARG cc_start: 0.9252 (mtm-85) cc_final: 0.9040 (mtm-85) REVERT: B 246 ASN cc_start: 0.9087 (OUTLIER) cc_final: 0.8644 (m110) REVERT: B 291 GLU cc_start: 0.8801 (OUTLIER) cc_final: 0.8237 (mp0) REVERT: B 339 LEU cc_start: 0.9247 (OUTLIER) cc_final: 0.8937 (mt) REVERT: B 550 SER cc_start: 0.8950 (OUTLIER) cc_final: 0.8710 (p) REVERT: B 619 GLU cc_start: 0.9033 (mm-30) cc_final: 0.8620 (mp0) REVERT: B 684 LYS cc_start: 0.7984 (OUTLIER) cc_final: 0.7762 (mtmm) REVERT: B 796 TRP cc_start: 0.8755 (t60) cc_final: 0.8261 (t-100) REVERT: B 797 TRP cc_start: 0.8317 (t60) cc_final: 0.7977 (t60) REVERT: B 824 SER cc_start: 0.8795 (m) cc_final: 0.8345 (t) outliers start: 38 outliers final: 19 residues processed: 92 average time/residue: 0.5626 time to fit residues: 57.0427 Evaluate side-chains 85 residues out of total 1436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 57 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 96 PHE Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 124 SER Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 236 MET Chi-restraints excluded: chain A residue 291 GLU Chi-restraints excluded: chain A residue 352 GLU Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 429 SER Chi-restraints excluded: chain A residue 491 CYS Chi-restraints excluded: chain A residue 602 MET Chi-restraints excluded: chain A residue 684 LYS Chi-restraints excluded: chain A residue 812 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 96 PHE Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 236 MET Chi-restraints excluded: chain B residue 246 ASN Chi-restraints excluded: chain B residue 291 GLU Chi-restraints excluded: chain B residue 339 LEU Chi-restraints excluded: chain B residue 352 GLU Chi-restraints excluded: chain B residue 429 SER Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 550 SER Chi-restraints excluded: chain B residue 602 MET Chi-restraints excluded: chain B residue 684 LYS Chi-restraints excluded: chain B residue 812 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: [75, 19, 9, 151, 51, 105, 33, 21, 84, 89, 143] chunk 75 optimal weight: 20.0000 chunk 19 optimal weight: 2.9990 chunk 9 optimal weight: 5.9990 chunk 151 optimal weight: 9.9990 chunk 51 optimal weight: 5.9990 chunk 105 optimal weight: 6.9990 chunk 33 optimal weight: 5.9990 chunk 21 optimal weight: 3.9990 chunk 84 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 chunk 143 optimal weight: 5.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 246 ASN ** A 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.092116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.063526 restraints weight = 24718.942| |-----------------------------------------------------------------------------| r_work (start): 0.2840 rms_B_bonded: 3.02 r_work: 0.2658 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8692 moved from start: 0.3497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.065 13352 Z= 0.331 Angle : 0.673 9.246 18186 Z= 0.334 Chirality : 0.049 0.208 2198 Planarity : 0.004 0.047 2216 Dihedral : 6.512 58.287 2598 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.40 % Allowed : 6.94 % Favored : 92.67 % Rotamer: Outliers : 2.79 % Allowed : 21.03 % Favored : 76.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.22 (0.22), residues: 1514 helix: -2.83 (0.34), residues: 158 sheet: -2.07 (0.32), residues: 284 loop : -0.02 (0.20), residues: 1072 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 121 TYR 0.013 0.002 TYR B 751 PHE 0.018 0.002 PHE A 785 TRP 0.013 0.002 TRP A 793 HIS 0.004 0.001 HIS A 298 Details of bonding type rmsd/Z covalent geometry : bond 0.00781 / 0.33 (13288) covalent geometry : angle 0.66121 / 0.33 (18024) SS BOND : bond 0.00722 / 0.54 ( 18) SS BOND : angle 0.96675 / 0.78 ( 36) hydrogen bonds : bond 0.04748 / 3.10 ( 154) hydrogen bonds : angle 5.30439 / 3.64 ( 294) Misc. bond : bond 0.00034 / 0.01 ( 4) link_ALPHA1-6 : bond 0.00893 / 0.45 ( 2) link_ALPHA1-6 : angle 1.21369 / 0.58 ( 6) link_BETA1-4 : bond 0.00428 / 0.27 ( 20) link_BETA1-4 : angle 1.63241 / 1.06 ( 60) link_NAG-ASN : bond 0.00636 / 0.43 ( 20) link_NAG-ASN : angle 1.56443 / 1.07 ( 60) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 1436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 55 time to evaluate : 0.523 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 96 PHE cc_start: 0.9205 (OUTLIER) cc_final: 0.8379 (t80) REVERT: A 291 GLU cc_start: 0.8903 (OUTLIER) cc_final: 0.8413 (mp0) REVERT: A 517 SER cc_start: 0.9340 (OUTLIER) cc_final: 0.9054 (p) REVERT: A 824 SER cc_start: 0.8991 (m) cc_final: 0.8570 (t) REVERT: B 40 LEU cc_start: 0.8549 (tp) cc_final: 0.8161 (tm) REVERT: B 96 PHE cc_start: 0.9204 (OUTLIER) cc_final: 0.8566 (t80) REVERT: B 121 ARG cc_start: 0.9203 (mtm-85) cc_final: 0.8991 (mtm-85) REVERT: B 246 ASN cc_start: 0.8981 (m-40) cc_final: 0.8537 (m110) REVERT: B 291 GLU cc_start: 0.8885 (OUTLIER) cc_final: 0.8404 (mp0) REVERT: B 339 LEU cc_start: 0.9484 (OUTLIER) cc_final: 0.9234 (mt) REVERT: B 517 SER cc_start: 0.9351 (OUTLIER) cc_final: 0.9073 (p) REVERT: B 684 LYS cc_start: 0.8418 (OUTLIER) cc_final: 0.8192 (mtmm) REVERT: B 797 TRP cc_start: 0.8569 (t60) cc_final: 0.8175 (t60) REVERT: B 824 SER cc_start: 0.9005 (m) cc_final: 0.8585 (t) outliers start: 40 outliers final: 17 residues processed: 86 average time/residue: 0.4973 time to fit residues: 47.7135 Evaluate side-chains 80 residues out of total 1436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 55 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 96 PHE Chi-restraints excluded: chain A residue 124 SER Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 236 MET Chi-restraints excluded: chain A residue 291 GLU Chi-restraints excluded: chain A residue 352 GLU Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 517 SER Chi-restraints excluded: chain A residue 756 SER Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 812 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 96 PHE Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 236 MET Chi-restraints excluded: chain B residue 291 GLU Chi-restraints excluded: chain B residue 339 LEU Chi-restraints excluded: chain B residue 352 GLU Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 517 SER Chi-restraints excluded: chain B residue 684 LYS Chi-restraints excluded: chain B residue 812 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: [40, 131, 143, 9, 77, 20, 17, 26, 91, 68, 65] chunk 40 optimal weight: 1.9990 chunk 131 optimal weight: 1.9990 chunk 143 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 77 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 91 optimal weight: 0.6980 chunk 68 optimal weight: 0.9980 chunk 65 optimal weight: 0.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 66 ASN ** A 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 246 ASN ** A 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 99 ASN B 137 ASN B 763 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.095310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.066557 restraints weight = 24104.465| |-----------------------------------------------------------------------------| r_work (start): 0.2894 rms_B_bonded: 3.08 r_work: 0.2713 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8633 moved from start: 0.3401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13352 Z= 0.119 Angle : 0.542 9.357 18186 Z= 0.274 Chirality : 0.043 0.148 2198 Planarity : 0.003 0.036 2216 Dihedral : 6.184 58.079 2598 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.40 % Allowed : 4.89 % Favored : 94.72 % Rotamer: Outliers : 1.88 % Allowed : 21.80 % Favored : 76.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.16 (0.23), residues: 1514 helix: -2.90 (0.33), residues: 162 sheet: -2.05 (0.32), residues: 284 loop : 0.06 (0.20), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 121 TYR 0.011 0.001 TYR B 546 PHE 0.024 0.001 PHE A 785 TRP 0.009 0.001 TRP B 797 HIS 0.004 0.001 HIS B 781 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 (13288) covalent geometry : angle 0.53364 / 0.27 (18024) SS BOND : bond 0.00327 / 0.24 ( 18) SS BOND : angle 0.71006 / 0.57 ( 36) hydrogen bonds : bond 0.03402 / 2.22 ( 154) hydrogen bonds : angle 5.16206 / 3.54 ( 294) Misc. bond : bond 0.00033 / 0.01 ( 4) link_ALPHA1-6 : bond 0.00730 / 0.37 ( 2) link_ALPHA1-6 : angle 1.31795 / 0.69 ( 6) link_BETA1-4 : bond 0.00442 / 0.30 ( 20) link_BETA1-4 : angle 1.33542 / 0.93 ( 60) link_NAG-ASN : bond 0.00199 / 0.13 ( 20) link_NAG-ASN : angle 1.15796 / 0.81 ( 60) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 1436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 58 time to evaluate : 0.504 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 96 PHE cc_start: 0.9171 (OUTLIER) cc_final: 0.8395 (t80) REVERT: A 246 ASN cc_start: 0.9165 (OUTLIER) cc_final: 0.8901 (m-40) REVERT: A 291 GLU cc_start: 0.8857 (OUTLIER) cc_final: 0.8379 (mp0) REVERT: A 824 SER cc_start: 0.8989 (m) cc_final: 0.8568 (t) REVERT: B 34 LEU cc_start: 0.8668 (mm) cc_final: 0.8437 (mm) REVERT: B 40 LEU cc_start: 0.8597 (tp) cc_final: 0.8246 (tm) REVERT: B 96 PHE cc_start: 0.9160 (OUTLIER) cc_final: 0.8604 (t80) REVERT: B 246 ASN cc_start: 0.9040 (m-40) cc_final: 0.8731 (m110) REVERT: B 291 GLU cc_start: 0.8848 (OUTLIER) cc_final: 0.8338 (mp0) REVERT: B 339 LEU cc_start: 0.9403 (OUTLIER) cc_final: 0.9160 (mt) REVERT: B 684 LYS cc_start: 0.8369 (OUTLIER) cc_final: 0.8103 (mtmm) REVERT: B 780 LEU cc_start: 0.8961 (mp) cc_final: 0.8716 (mm) REVERT: B 797 TRP cc_start: 0.8527 (t60) cc_final: 0.8149 (t60) REVERT: B 824 SER cc_start: 0.9011 (m) cc_final: 0.8588 (t) outliers start: 27 outliers final: 13 residues processed: 78 average time/residue: 0.5041 time to fit residues: 43.7753 Evaluate side-chains 75 residues out of total 1436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 55 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 96 PHE Chi-restraints excluded: chain A residue 124 SER Chi-restraints excluded: chain A residue 236 MET Chi-restraints excluded: chain A residue 246 ASN Chi-restraints excluded: chain A residue 291 GLU Chi-restraints excluded: chain A residue 352 GLU Chi-restraints excluded: chain A residue 812 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 96 PHE Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 236 MET Chi-restraints excluded: chain B residue 291 GLU Chi-restraints excluded: chain B residue 339 LEU Chi-restraints excluded: chain B residue 352 GLU Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 684 LYS Chi-restraints excluded: chain B residue 812 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: [147, 124, 64, 41, 125, 86, 140, 49, 52, 94, 4] chunk 147 optimal weight: 3.9990 chunk 124 optimal weight: 0.9980 chunk 64 optimal weight: 5.9990 chunk 41 optimal weight: 8.9990 chunk 125 optimal weight: 5.9990 chunk 86 optimal weight: 8.9990 chunk 140 optimal weight: 5.9990 chunk 49 optimal weight: 4.9990 chunk 52 optimal weight: 3.9990 chunk 94 optimal weight: 2.9990 chunk 4 optimal weight: 4.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 246 ASN ** A 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 99 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.092270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.064187 restraints weight = 24967.823| |-----------------------------------------------------------------------------| r_work (start): 0.2930 rms_B_bonded: 3.01 r_work: 0.2737 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.2737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8727 moved from start: 0.3617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.058 13352 Z= 0.300 Angle : 0.646 8.758 18186 Z= 0.321 Chirality : 0.048 0.189 2198 Planarity : 0.004 0.040 2216 Dihedral : 6.293 58.053 2598 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.40 % Allowed : 7.00 % Favored : 92.60 % Rotamer: Outliers : 1.95 % Allowed : 21.73 % Favored : 76.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.34 (0.22), residues: 1514 helix: -2.92 (0.32), residues: 172 sheet: -2.09 (0.32), residues: 284 loop : -0.07 (0.20), residues: 1058 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 121 TYR 0.012 0.002 TYR A 233 PHE 0.019 0.002 PHE A 785 TRP 0.010 0.001 TRP A 793 HIS 0.005 0.001 HIS A 298 Details of bonding type rmsd/Z covalent geometry : bond 0.00710 / 0.30 (13288) covalent geometry : angle 0.63319 / 0.32 (18024) SS BOND : bond 0.00633 / 0.47 ( 18) SS BOND : angle 1.44837 / 1.11 ( 36) hydrogen bonds : bond 0.04455 / 2.91 ( 154) hydrogen bonds : angle 5.23759 / 3.59 ( 294) Misc. bond : bond 0.00018 / 0.01 ( 4) link_ALPHA1-6 : bond 0.00857 / 0.43 ( 2) link_ALPHA1-6 : angle 1.19612 / 0.59 ( 6) link_BETA1-4 : bond 0.00411 / 0.26 ( 20) link_BETA1-4 : angle 1.54406 / 1.02 ( 60) link_NAG-ASN : bond 0.00571 / 0.39 ( 20) link_NAG-ASN : angle 1.47503 / 1.00 ( 60) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 1436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 56 time to evaluate : 0.307 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 96 PHE cc_start: 0.9230 (OUTLIER) cc_final: 0.8464 (t80) REVERT: A 291 GLU cc_start: 0.8906 (OUTLIER) cc_final: 0.8426 (mp0) REVERT: A 824 SER cc_start: 0.8947 (m) cc_final: 0.8496 (t) REVERT: B 34 LEU cc_start: 0.8644 (mm) cc_final: 0.8365 (mm) REVERT: B 40 LEU cc_start: 0.8637 (tp) cc_final: 0.8291 (tm) REVERT: B 96 PHE cc_start: 0.9226 (OUTLIER) cc_final: 0.8598 (t80) REVERT: B 246 ASN cc_start: 0.9078 (m-40) cc_final: 0.8781 (m110) REVERT: B 291 GLU cc_start: 0.8889 (OUTLIER) cc_final: 0.8425 (mp0) REVERT: B 339 LEU cc_start: 0.9481 (OUTLIER) cc_final: 0.9221 (mt) REVERT: B 684 LYS cc_start: 0.8416 (OUTLIER) cc_final: 0.8215 (mtmm) REVERT: B 797 TRP cc_start: 0.8628 (t60) cc_final: 0.8280 (t60) REVERT: B 824 SER cc_start: 0.8975 (m) cc_final: 0.8543 (t) outliers start: 28 outliers final: 17 residues processed: 75 average time/residue: 0.5883 time to fit residues: 48.6678 Evaluate side-chains 75 residues out of total 1436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 52 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 96 PHE Chi-restraints excluded: chain A residue 124 SER Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 291 GLU Chi-restraints excluded: chain A residue 352 GLU Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 602 MET Chi-restraints excluded: chain A residue 812 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 96 PHE Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 236 MET Chi-restraints excluded: chain B residue 291 GLU Chi-restraints excluded: chain B residue 339 LEU Chi-restraints excluded: chain B residue 352 GLU Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 602 MET Chi-restraints excluded: chain B residue 684 LYS Chi-restraints excluded: chain B residue 756 SER Chi-restraints excluded: chain B residue 812 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: [23, 17, 58, 144, 26, 12, 82, 142, 50, 99, 92] chunk 23 optimal weight: 0.9980 chunk 17 optimal weight: 0.9990 chunk 58 optimal weight: 0.7980 chunk 144 optimal weight: 0.6980 chunk 26 optimal weight: 0.6980 chunk 12 optimal weight: 5.9990 chunk 82 optimal weight: 10.0000 chunk 142 optimal weight: 0.0070 chunk 50 optimal weight: 2.9990 chunk 99 optimal weight: 0.0050 chunk 92 optimal weight: 0.7980 overall best weight: 0.4412 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 137 ASN ** B 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 99 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.095807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.067567 restraints weight = 24445.035| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 3.03 r_work: 0.2814 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.3509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 13352 Z= 0.093 Angle : 0.547 9.229 18186 Z= 0.277 Chirality : 0.042 0.144 2198 Planarity : 0.004 0.059 2216 Dihedral : 5.665 56.059 2598 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.40 % Allowed : 4.82 % Favored : 94.78 % Rotamer: Outliers : 1.46 % Allowed : 22.21 % Favored : 76.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.14 (0.23), residues: 1514 helix: -2.80 (0.34), residues: 162 sheet: -2.03 (0.32), residues: 282 loop : 0.05 (0.20), residues: 1070 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG B 114 TYR 0.011 0.001 TYR A 546 PHE 0.026 0.001 PHE A 785 TRP 0.007 0.001 TRP B 797 HIS 0.003 0.001 HIS A 298 Details of bonding type rmsd/Z covalent geometry : bond 0.00209 / 0.09 (13288) covalent geometry : angle 0.53801 / 0.28 (18024) SS BOND : bond 0.00261 / 0.19 ( 18) SS BOND : angle 1.06615 / 0.80 ( 36) hydrogen bonds : bond 0.02993 / 1.95 ( 154) hydrogen bonds : angle 5.05434 / 3.46 ( 294) Misc. bond : bond 0.00052 / 0.02 ( 4) link_ALPHA1-6 : bond 0.00655 / 0.33 ( 2) link_ALPHA1-6 : angle 1.35819 / 0.74 ( 6) link_BETA1-4 : bond 0.00451 / 0.31 ( 20) link_BETA1-4 : angle 1.30970 / 0.92 ( 60) link_NAG-ASN : bond 0.00161 / 0.10 ( 20) link_NAG-ASN : angle 1.08963 / 0.77 ( 60) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 1436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 52 time to evaluate : 0.456 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 40 LEU cc_start: 0.8911 (mm) cc_final: 0.8633 (tm) REVERT: A 96 PHE cc_start: 0.9172 (OUTLIER) cc_final: 0.8477 (t80) REVERT: A 291 GLU cc_start: 0.8846 (OUTLIER) cc_final: 0.8362 (mp0) REVERT: B 40 LEU cc_start: 0.8622 (tp) cc_final: 0.8259 (tm) REVERT: B 96 PHE cc_start: 0.9174 (OUTLIER) cc_final: 0.8556 (t80) REVERT: B 246 ASN cc_start: 0.9021 (m-40) cc_final: 0.8738 (m110) REVERT: B 291 GLU cc_start: 0.8837 (OUTLIER) cc_final: 0.8330 (mp0) REVERT: B 339 LEU cc_start: 0.9381 (OUTLIER) cc_final: 0.9093 (mt) REVERT: B 684 LYS cc_start: 0.8438 (OUTLIER) cc_final: 0.8177 (mtmm) REVERT: B 797 TRP cc_start: 0.8566 (t60) cc_final: 0.8188 (t60) outliers start: 21 outliers final: 9 residues processed: 66 average time/residue: 0.6070 time to fit residues: 44.2260 Evaluate side-chains 65 residues out of total 1436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 50 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 96 PHE Chi-restraints excluded: chain A residue 124 SER Chi-restraints excluded: chain A residue 291 GLU Chi-restraints excluded: chain A residue 352 GLU Chi-restraints excluded: chain A residue 812 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 96 PHE Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 236 MET Chi-restraints excluded: chain B residue 291 GLU Chi-restraints excluded: chain B residue 339 LEU Chi-restraints excluded: chain B residue 352 GLU Chi-restraints excluded: chain B residue 684 LYS Chi-restraints excluded: chain B residue 812 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: [9, 34, 132, 125, 65, 99, 20, 37, 7, 116, 87] chunk 9 optimal weight: 0.9990 chunk 34 optimal weight: 0.9980 chunk 132 optimal weight: 0.9990 chunk 125 optimal weight: 4.9990 chunk 65 optimal weight: 0.9990 chunk 99 optimal weight: 0.9990 chunk 20 optimal weight: 4.9990 chunk 37 optimal weight: 0.7980 chunk 7 optimal weight: 0.9990 chunk 116 optimal weight: 4.9990 chunk 87 optimal weight: 7.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 99 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.095571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.067594 restraints weight = 24424.285| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 3.01 r_work: 0.2805 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8709 moved from start: 0.3521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13352 Z= 0.111 Angle : 0.534 9.315 18186 Z= 0.270 Chirality : 0.042 0.143 2198 Planarity : 0.003 0.047 2216 Dihedral : 5.273 55.390 2598 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.40 % Allowed : 4.95 % Favored : 94.65 % Rotamer: Outliers : 1.25 % Allowed : 22.21 % Favored : 76.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.12 (0.23), residues: 1514 helix: -2.77 (0.33), residues: 162 sheet: -1.99 (0.32), residues: 282 loop : 0.05 (0.20), residues: 1070 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 121 TYR 0.010 0.001 TYR A 546 PHE 0.020 0.001 PHE A 785 TRP 0.007 0.001 TRP B 797 HIS 0.003 0.000 HIS B 781 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.11 (13288) covalent geometry : angle 0.52508 / 0.27 (18024) SS BOND : bond 0.00292 / 0.22 ( 18) SS BOND : angle 0.96342 / 0.73 ( 36) hydrogen bonds : bond 0.03094 / 2.01 ( 154) hydrogen bonds : angle 5.01372 / 3.42 ( 294) Misc. bond : bond 0.00040 / 0.01 ( 4) link_ALPHA1-6 : bond 0.00697 / 0.35 ( 2) link_ALPHA1-6 : angle 1.31529 / 0.71 ( 6) link_BETA1-4 : bond 0.00430 / 0.29 ( 20) link_BETA1-4 : angle 1.34986 / 0.92 ( 60) link_NAG-ASN : bond 0.00170 / 0.11 ( 20) link_NAG-ASN : angle 1.08988 / 0.77 ( 60) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3479.74 seconds wall clock time: 60 minutes 12.71 seconds (3612.71 seconds total)