Starting phenix.real_space_refine on Sun Jul 5 11:16:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7akd_11812/07_2026/7akd_11812.cif Found real_map, /net/cci-nas-00/data/ceres_data/7akd_11812/07_2026/7akd_11812.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7akd_11812/07_2026/7akd_11812.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7akd_11812/07_2026/7akd_11812.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7akd_11812/07_2026/7akd_11812.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7akd_11812/07_2026/7akd_11812.cif" model { file = "/net/cci-nas-00/data/ceres_data/7akd_11812/07_2026/7akd_11812.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7akd_11812/07_2026/7akd_11812.cif" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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: 4 Type Number sf(0) Gaussians S 112 5.16 5 C 17403 2.51 5 N 4439 2.21 5 O 5404 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 54 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 27358 Number of models: 1 Model: "" Number of chains: 29 Chain: "A" Number of atoms: 7517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 970, 7517 Classifications: {'peptide': 970} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 48, 'TRANS': 921} Chain breaks: 9 Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 83 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 3, 'ASN:plan1': 4, 'GLU:plan': 4, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 45 Chain: "B" Number of atoms: 7666 Number of conformers: 1 Conformer: "" Number of residues, atoms: 990, 7666 Classifications: {'peptide': 990} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 49, 'TRANS': 940} Chain breaks: 7 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASN:plan1': 3, 'GLN:plan1': 2, 'GLU:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 35 Chain: "C" Number of atoms: 7685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 992, 7685 Classifications: {'peptide': 992} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 49, 'TRANS': 942} Chain breaks: 8 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 75 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 3, 'PHE:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 4} Unresolved non-hydrogen planarities: 40 Chain: "D" Number of atoms: 925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 925 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 6, 'TRANS': 113} Chain: "E" Number of atoms: 798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 798 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 98} Chain: "H" Number of atoms: 925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 925 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 6, 'TRANS': 113} Chain: "L" Number of atoms: 798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 798 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 98} 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 chiralities: 2 Chain: "G" 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 chiralities: 3 Chain: "I" 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 chiralities: 3 Chain: "J" 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 chiralities: 2 Chain: "K" 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 chiralities: 2 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 chiralities: 2 Chain: "N" 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 chiralities: 3 Chain: "O" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 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 chiralities: 2 Chain: "Q" 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 chiralities: 2 Chain: "R" 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 chiralities: 2 Chain: "S" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "T" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 71 Unusual residues: {'BMA': 1, 'FUC': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Chain: "U" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {'MAN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "V" 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 chiralities: 2 Chain: "W" 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 chiralities: 2 Chain: "X" 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 chiralities: 2 Chain: "A" Number of atoms: 136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 136 Unusual residues: {'FUC': 1, 'NAG': 9} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 Chain: "B" Number of atoms: 178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 178 Unusual residues: {'FUC': 1, 'NAG': 12} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen chiralities: 13 Chain: "C" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 108 Unusual residues: {'FUC': 1, 'NAG': 7} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Chain: "D" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Unusual residues: {'MAN': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "H" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Unusual residues: {'MAN': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 5.69, per 1000 atoms: 0.21 Number of scatterers: 27358 At special positions: 0 Unit cell: (156.6, 143.64, 191.16, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 112 16.00 O 5404 8.00 N 4439 7.00 C 17403 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.04 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.02 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 95 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 95 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " 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=1, symmetry=0 Links applied ALPHA1-3 " BMA O 3 " - " MAN O 4 " " MAN T 4 " - " MAN T 5 " ALPHA1-6 " BMA T 3 " - " MAN T 4 " " MAN U 1 " - " MAN U 2 " BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " BETA1-6 " NAG S 1 " - " FUC S 4 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG T 1 " - " FUC T 6 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 165 " " NAG A1304 " - " ASN A 616 " " NAG A1305 " - " ASN A 657 " " NAG A1306 " - " ASN A 709 " " NAG A1307 " - " ASN A 717 " " NAG A1309 " - " ASN A1074 " " NAG B1301 " - " ASN B 61 " " NAG B1304 " - " ASN B 234 " " NAG B1307 " - " ASN B 616 " " NAG B1308 " - " ASN B 657 " " NAG B1310 " - " ASN B 717 " " NAG C1303 " - " ASN C 331 " " NAG C1304 " - " ASN C 616 " " NAG C1307 " - " ASN C 801 " " NAG F 1 " - " ASN A 234 " " NAG G 1 " - " ASN A 282 " " NAG I 1 " - " ASN A 331 " " NAG J 1 " - " ASN A 343 " " NAG M 1 " - " ASN A1098 " " NAG N 1 " - " ASN B 282 " " NAG O 1 " - " ASN B 343 " " NAG Q 1 " - " ASN B1098 " " NAG S 1 " - " ASN C 282 " " NAG T 1 " - " ASN C 343 " " NAG W 1 " - " ASN C1074 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.50 Conformation dependent library (CDL) restraints added in 1.1 seconds 6684 Ramachandran restraints generated. 3342 Oldfield, 0 Emsley, 3342 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6352 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 57 sheets defined 24.6% alpha, 28.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.34 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 364 through 371 removed outlier: 4.421A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.003A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 removed outlier: 4.087A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 782 removed outlier: 4.614A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LYS A 776 " --> pdb=" O VAL A 772 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLN A 779 " --> pdb=" O ASP A 775 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VAL A 781 " --> pdb=" O ASN A 777 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N PHE A 782 " --> pdb=" O THR A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 825 removed outlier: 3.513A pdb=" N ASP A 820 " --> pdb=" O SER A 816 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU A 821 " --> pdb=" O PHE A 817 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 884 removed outlier: 3.570A pdb=" N ILE A 882 " --> pdb=" O LEU A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.899A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 908 removed outlier: 3.521A pdb=" N GLN A 901 " --> pdb=" O PRO A 897 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N MET A 902 " --> pdb=" O PHE A 898 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ALA A 903 " --> pdb=" O ALA A 899 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASN A 907 " --> pdb=" O ALA A 903 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 941 removed outlier: 3.873A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N GLU A 918 " --> pdb=" O ASN A 914 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASN A 919 " --> pdb=" O VAL A 915 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N LYS A 921 " --> pdb=" O TYR A 917 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N LEU A 922 " --> pdb=" O GLU A 918 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N THR A 941 " --> pdb=" O SER A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 945 Processing helix chain 'A' and resid 946 through 965 removed outlier: 3.593A pdb=" N ASP A 950 " --> pdb=" O GLY A 946 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.564A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ARG A 983 " --> pdb=" O ASP A 979 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 3.973A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N ASP A 994 " --> pdb=" O GLU A 990 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N ALA A1016 " --> pdb=" O LEU A1012 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N GLU A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ILE A1018 " --> pdb=" O ARG A1014 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL A1033 " --> pdb=" O MET A1029 " (cutoff:3.500A) Processing helix chain 'A' and resid 1116 through 1118 No H-bonds generated for 'chain 'A' and resid 1116 through 1118' Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 4.330A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 338 through 344 removed outlier: 3.880A pdb=" N PHE B 342 " --> pdb=" O PHE B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.882A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 371 removed outlier: 3.913A pdb=" N TYR B 369 " --> pdb=" O TYR B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 389 removed outlier: 3.775A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 3.966A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 616 through 620 Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 removed outlier: 4.107A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LEU B 754 " --> pdb=" O SER B 750 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 782 removed outlier: 3.673A pdb=" N VAL B 772 " --> pdb=" O THR B 768 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N GLU B 773 " --> pdb=" O GLY B 769 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N GLN B 774 " --> pdb=" O ILE B 770 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LYS B 776 " --> pdb=" O VAL B 772 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.913A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 884 removed outlier: 3.774A pdb=" N SER B 875 " --> pdb=" O ALA B 871 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 906 removed outlier: 3.878A pdb=" N ALA B 903 " --> pdb=" O ALA B 899 " (cutoff:3.500A) Processing helix chain 'B' and resid 907 through 910 removed outlier: 3.616A pdb=" N GLY B 910 " --> pdb=" O ASN B 907 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 907 through 910' Processing helix chain 'B' and resid 913 through 918 Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.556A pdb=" N ILE B 923 " --> pdb=" O ASN B 919 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLY B 932 " --> pdb=" O ASN B 928 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LYS B 933 " --> pdb=" O SER B 929 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N THR B 941 " --> pdb=" O SER B 937 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.752A pdb=" N GLN B 949 " --> pdb=" O LEU B 945 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ASN B 955 " --> pdb=" O VAL B 951 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 3.827A pdb=" N GLU B 990 " --> pdb=" O PRO B 986 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N ASP B 994 " --> pdb=" O GLU B 990 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLN B1002 " --> pdb=" O THR B 998 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE B1013 " --> pdb=" O THR B1009 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ALA B1020 " --> pdb=" O ALA B1016 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N SER B1021 " --> pdb=" O GLU B1017 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL B1033 " --> pdb=" O MET B1029 " (cutoff:3.500A) Processing helix chain 'B' and resid 1116 through 1118 No H-bonds generated for 'chain 'B' and resid 1116 through 1118' Processing helix chain 'B' and resid 1140 through 1146 removed outlier: 4.477A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 removed outlier: 3.811A pdb=" N PHE C 342 " --> pdb=" O PHE C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.731A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 367 through 371 removed outlier: 4.005A pdb=" N SER C 371 " --> pdb=" O LEU C 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 389 removed outlier: 4.352A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ASP C 389 " --> pdb=" O LYS C 386 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.146A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 removed outlier: 3.671A pdb=" N SER C 443 " --> pdb=" O ASN C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 737 through 744 removed outlier: 3.540A pdb=" N TYR C 741 " --> pdb=" O ASP C 737 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N ILE C 742 " --> pdb=" O CYS C 738 " (cutoff:3.500A) Processing helix chain 'C' and resid 746 through 754 removed outlier: 4.313A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.657A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU C 763 " --> pdb=" O PHE C 759 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLN C 774 " --> pdb=" O ILE C 770 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LYS C 776 " --> pdb=" O VAL C 772 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.713A pdb=" N ASP C 820 " --> pdb=" O SER C 816 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU C 821 " --> pdb=" O PHE C 817 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 removed outlier: 4.040A pdb=" N LEU C 878 " --> pdb=" O THR C 874 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N THR C 883 " --> pdb=" O ALA C 879 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLY C 885 " --> pdb=" O THR C 881 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 908 removed outlier: 3.753A pdb=" N ALA C 903 " --> pdb=" O ALA C 899 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 918 removed outlier: 3.685A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.767A pdb=" N THR C 941 " --> pdb=" O SER C 937 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.533A pdb=" N GLN C 949 " --> pdb=" O LEU C 945 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ASN C 955 " --> pdb=" O VAL C 951 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA C 958 " --> pdb=" O GLN C 954 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL C 963 " --> pdb=" O LEU C 959 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.114A pdb=" N GLU C 990 " --> pdb=" O PRO C 986 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N GLN C1002 " --> pdb=" O THR C 998 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N TYR C1007 " --> pdb=" O SER C1003 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLN C1010 " --> pdb=" O THR C1006 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ILE C1013 " --> pdb=" O THR C1009 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ALA C1020 " --> pdb=" O ALA C1016 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N SER C1021 " --> pdb=" O GLU C1017 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1147 removed outlier: 3.657A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 75 No H-bonds generated for 'chain 'D' and resid 73 through 75' Processing helix chain 'D' and resid 86 through 90 removed outlier: 3.828A pdb=" N THR D 90 " --> pdb=" O ALA D 87 " (cutoff:3.500A) Processing helix chain 'E' and resid 79 through 83 Processing helix chain 'H' and resid 73 through 75 No H-bonds generated for 'chain 'H' and resid 73 through 75' Processing helix chain 'H' and resid 86 through 90 removed outlier: 3.827A pdb=" N THR H 90 " --> pdb=" O ALA H 87 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 3.643A pdb=" N GLU A 96 " --> pdb=" O ASN A 188 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ASN A 188 " --> pdb=" O GLU A 96 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU A 226 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N SER A 205 " --> pdb=" O GLU A 224 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.854A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.866A pdb=" N ARG A 237 " --> pdb=" O GLY A 107 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLY A 107 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 311 through 319 removed outlier: 3.575A pdb=" N THR A 599 " --> pdb=" O GLY A 311 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 324 through 328 removed outlier: 6.455A pdb=" N GLU A 324 " --> pdb=" O ASN A 540 " (cutoff:3.500A) removed outlier: 8.419A pdb=" N ASN A 542 " --> pdb=" O GLU A 324 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ILE A 326 " --> pdb=" O ASN A 542 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N THR A 572 " --> pdb=" O ASP A 568 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 354 through 358 removed outlier: 6.652A pdb=" N ASN A 437 " --> pdb=" O PHE A 374 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N PHE A 374 " --> pdb=" O ASN A 437 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.696A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 453 through 454 Processing sheet with id=AA9, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.216A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 702 through 704 Processing sheet with id=AB2, first strand: chain 'A' and resid 712 through 715 Processing sheet with id=AB3, first strand: chain 'A' and resid 718 through 728 removed outlier: 3.513A pdb=" N ALA A1056 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB5, first strand: chain 'A' and resid 788 through 790 removed outlier: 6.067A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'A' and resid 1120 through 1123 removed outlier: 3.594A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AB8, first strand: chain 'B' and resid 28 through 29 removed outlier: 3.899A pdb=" N THR B 29 " --> pdb=" O VAL B 62 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N VAL B 62 " --> pdb=" O THR B 29 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TYR B 265 " --> pdb=" O PHE B 65 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA B 93 " --> pdb=" O TYR B 266 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.997A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.704A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 47 through 55 removed outlier: 4.108A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 83 through 85 removed outlier: 3.701A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU B 117 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N PHE B 133 " --> pdb=" O SER B 112 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N THR B 114 " --> pdb=" O CYS B 131 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N CYS B 131 " --> pdb=" O THR B 114 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N SER B 116 " --> pdb=" O LYS B 129 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N LYS B 129 " --> pdb=" O SER B 116 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N LEU B 118 " --> pdb=" O VAL B 127 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N VAL B 127 " --> pdb=" O LEU B 118 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N GLU B 132 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N CYS B 166 " --> pdb=" O GLU B 132 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.637A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 325 through 328 removed outlier: 5.944A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AC5, first strand: chain 'B' and resid 391 through 392 Processing sheet with id=AC6, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC7, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC8, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.606A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 702 through 704 Processing sheet with id=AD1, first strand: chain 'B' and resid 711 through 718 removed outlier: 6.477A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N ASN B 717 " --> pdb=" O ALA B1070 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 721 through 728 removed outlier: 3.606A pdb=" N ALA B1056 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 734 through 735 Processing sheet with id=AD4, first strand: chain 'B' and resid 1120 through 1122 removed outlier: 3.618A pdb=" N ILE B1081 " --> pdb=" O HIS B1088 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 28 through 30 removed outlier: 8.702A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N TYR C 265 " --> pdb=" O PHE C 65 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.990A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.573A pdb=" N LEU C 84 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.521A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL C 610 " --> pdb=" O ILE C 651 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 325 through 328 removed outlier: 3.825A pdb=" N PHE C 543 " --> pdb=" O LEU C 546 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 356 through 358 removed outlier: 3.670A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.839A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE4, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.470A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.794A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 711 through 713 Processing sheet with id=AE6, first strand: chain 'C' and resid 719 through 728 removed outlier: 3.681A pdb=" N VAL C1068 " --> pdb=" O THR C 719 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 719 through 728 removed outlier: 3.681A pdb=" N VAL C1068 " --> pdb=" O THR C 719 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 1120 through 1123 removed outlier: 3.640A pdb=" N ILE C1081 " --> pdb=" O HIS C1088 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id=AF1, first strand: chain 'D' and resid 3 through 7 removed outlier: 3.537A pdb=" N GLN D 77 " --> pdb=" O ASP D 72 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'D' and resid 11 through 12 removed outlier: 6.672A pdb=" N TRP D 34 " --> pdb=" O TYR D 50 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N TYR D 50 " --> pdb=" O TRP D 34 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N TRP D 36 " --> pdb=" O ILE D 48 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'D' and resid 11 through 12 removed outlier: 6.920A pdb=" N CYS D 95 " --> pdb=" O TRP D 111 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N TRP D 111 " --> pdb=" O CYS D 95 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N ARG D 97 " --> pdb=" O GLU D 109 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'E' and resid 4 through 7 removed outlier: 3.878A pdb=" N SER E 22 " --> pdb=" O SER E 7 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'E' and resid 10 through 11 removed outlier: 3.515A pdb=" N ALA E 84 " --> pdb=" O VAL E 104 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ILE E 48 " --> pdb=" O TRP E 35 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N GLN E 37 " --> pdb=" O LEU E 46 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N LEU E 46 " --> pdb=" O GLN E 37 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'E' and resid 10 through 11 removed outlier: 3.515A pdb=" N ALA E 84 " --> pdb=" O VAL E 104 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLN E 90 " --> pdb=" O THR E 97 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N THR E 97 " --> pdb=" O GLN E 90 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.537A pdb=" N GLN H 77 " --> pdb=" O ASP H 72 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.672A pdb=" N TRP H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N TYR H 50 " --> pdb=" O TRP H 34 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.919A pdb=" N CYS H 95 " --> pdb=" O TRP H 111 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N TRP H 111 " --> pdb=" O CYS H 95 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N ARG H 97 " --> pdb=" O GLU H 109 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.879A pdb=" N SER L 22 " --> pdb=" O SER L 7 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'L' and resid 10 through 11 removed outlier: 3.514A pdb=" N ALA L 84 " --> pdb=" O VAL L 104 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ILE L 48 " --> pdb=" O TRP L 35 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N GLN L 37 " --> pdb=" O LEU L 46 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N LEU L 46 " --> pdb=" O GLN L 37 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'L' and resid 10 through 11 removed outlier: 3.514A pdb=" N ALA L 84 " --> pdb=" O VAL L 104 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLN L 90 " --> pdb=" O THR L 97 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) 1056 hydrogen bonds defined for protein. 2808 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.09 Time building geometry restraints manager: 3.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 8594 1.35 - 1.47: 7398 1.47 - 1.60: 11826 1.60 - 1.72: 1 1.72 - 1.85: 140 Bond restraints: 27959 Sorted by residual: bond pdb=" C1 FUC T 6 " pdb=" C2 FUC T 6 " ideal model delta sigma weight residual 1.528 1.622 -0.094 2.00e-02 2.50e+03 2.19e+01 bond pdb=" C1 FUC T 6 " pdb=" O5 FUC T 6 " ideal model delta sigma weight residual 1.400 1.481 -0.081 2.00e-02 2.50e+03 1.64e+01 bond pdb=" C1 MAN U 2 " pdb=" O5 MAN U 2 " ideal model delta sigma weight residual 1.399 1.450 -0.051 2.00e-02 2.50e+03 6.42e+00 bond pdb=" C1 BMA O 3 " pdb=" C2 BMA O 3 " ideal model delta sigma weight residual 1.519 1.569 -0.050 2.00e-02 2.50e+03 6.27e+00 bond pdb=" C1 MAN U 2 " pdb=" C2 MAN U 2 " ideal model delta sigma weight residual 1.526 1.576 -0.050 2.00e-02 2.50e+03 6.24e+00 ... (remaining 27954 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.11: 37218 2.11 - 4.21: 740 4.21 - 6.32: 101 6.32 - 8.43: 13 8.43 - 10.53: 2 Bond angle restraints: 38074 Sorted by residual: angle pdb=" N VAL A 608 " pdb=" CA VAL A 608 " pdb=" CB VAL A 608 " ideal model delta sigma weight residual 112.32 104.67 7.65 1.15e+00 7.56e-01 4.42e+01 angle pdb=" N ASN A 606 " pdb=" CA ASN A 606 " pdb=" C ASN A 606 " ideal model delta sigma weight residual 110.06 117.00 -6.94 1.43e+00 4.89e-01 2.36e+01 angle pdb=" C ASN A 606 " pdb=" CA ASN A 606 " pdb=" CB ASN A 606 " ideal model delta sigma weight residual 111.97 102.93 9.04 1.99e+00 2.53e-01 2.06e+01 angle pdb=" N VAL C 608 " pdb=" CA VAL C 608 " pdb=" CB VAL C 608 " ideal model delta sigma weight residual 112.32 107.50 4.82 1.15e+00 7.56e-01 1.76e+01 angle pdb=" N ILE H 110 " pdb=" CA ILE H 110 " pdb=" CB ILE H 110 " ideal model delta sigma weight residual 111.41 116.96 -5.55 1.38e+00 5.25e-01 1.62e+01 ... (remaining 38069 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 14922 17.92 - 35.83: 824 35.83 - 53.75: 152 53.75 - 71.67: 50 71.67 - 89.58: 40 Dihedral angle restraints: 15988 sinusoidal: 6114 harmonic: 9874 Sorted by residual: dihedral pdb=" CB CYS A1082 " pdb=" SG CYS A1082 " pdb=" SG CYS A1126 " pdb=" CB CYS A1126 " ideal model delta sinusoidal sigma weight residual -86.00 -149.74 63.74 1 1.00e+01 1.00e-02 5.35e+01 dihedral pdb=" CB CYS B 480 " pdb=" SG CYS B 480 " pdb=" SG CYS B 488 " pdb=" CB CYS B 488 " ideal model delta sinusoidal sigma weight residual 93.00 152.90 -59.90 1 1.00e+01 1.00e-02 4.79e+01 dihedral pdb=" CB CYS B1032 " pdb=" SG CYS B1032 " pdb=" SG CYS B1043 " pdb=" CB CYS B1043 " ideal model delta sinusoidal sigma weight residual 93.00 147.14 -54.14 1 1.00e+01 1.00e-02 3.98e+01 ... (remaining 15985 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.144: 4511 0.144 - 0.287: 46 0.287 - 0.431: 8 0.431 - 0.575: 1 0.575 - 0.719: 1 Chirality restraints: 4567 Sorted by residual: chirality pdb=" C1 NAG I 1 " pdb=" ND2 ASN A 331 " pdb=" C2 NAG I 1 " pdb=" O5 NAG I 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.68 -0.72 2.00e-01 2.50e+01 1.29e+01 chirality pdb=" C1 NAG S 1 " pdb=" ND2 ASN C 282 " pdb=" C2 NAG S 1 " pdb=" O5 NAG S 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.92 -0.48 2.00e-01 2.50e+01 5.81e+00 chirality pdb=" C1 NAG O 1 " pdb=" ND2 ASN B 343 " pdb=" C2 NAG O 1 " pdb=" O5 NAG O 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.97 -0.43 2.00e-01 2.50e+01 4.55e+00 ... (remaining 4564 not shown) Planarity restraints: 4816 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE C 714 " 0.068 5.00e-02 4.00e+02 1.03e-01 1.71e+01 pdb=" N PRO C 715 " -0.179 5.00e-02 4.00e+02 pdb=" CA PRO C 715 " 0.056 5.00e-02 4.00e+02 pdb=" CD PRO C 715 " 0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA CYS A 760 " -0.015 2.00e-02 2.50e+03 3.06e-02 9.37e+00 pdb=" C CYS A 760 " 0.053 2.00e-02 2.50e+03 pdb=" O CYS A 760 " -0.020 2.00e-02 2.50e+03 pdb=" N THR A 761 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY C1059 " 0.014 2.00e-02 2.50e+03 2.84e-02 8.09e+00 pdb=" C GLY C1059 " -0.049 2.00e-02 2.50e+03 pdb=" O GLY C1059 " 0.019 2.00e-02 2.50e+03 pdb=" N VAL C1060 " 0.016 2.00e-02 2.50e+03 ... (remaining 4813 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 440 2.68 - 3.24: 25814 3.24 - 3.79: 37203 3.79 - 4.35: 49724 4.35 - 4.90: 85238 Nonbonded interactions: 198419 Sorted by model distance: nonbonded pdb=" OD1 ASN B 360 " pdb=" OG1 THR B 523 " model vdw 2.126 3.040 nonbonded pdb=" O GLU A 661 " pdb=" OH TYR A 695 " model vdw 2.138 3.040 nonbonded pdb=" OG SER C 708 " pdb=" OG SER C 711 " model vdw 2.141 3.040 nonbonded pdb=" OH TYR C 91 " pdb=" OE1 GLU C 191 " model vdw 2.201 3.040 nonbonded pdb=" OD1 ASN B 343 " pdb=" N2 NAG O 1 " model vdw 2.221 3.120 ... (remaining 198414 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 66 or resid 82 through 96 or (resid 97 and (nam \ e N or name CA or name C or name O or name CB )) or resid 98 through 109 or (res \ id 110 through 111 and (name N or name CA or name C or name O or name CB )) or r \ esid 112 through 113 or resid 116 through 128 or (resid 129 and (name N or name \ CA or name C or name O or name CB )) or resid 130 through 134 or (resid 135 thro \ ugh 138 and (name N or name CA or name C or name O or name CB )) or resid 139 th \ rough 140 or resid 166 through 172 or resid 187 through 241 or (resid 242 throug \ h 263 and (name N or name CA or name C or name O or name CB )) or resid 265 thro \ ugh 613 or (resid 614 and (name N or name CA or name C or name O or name CB )) o \ r resid 615 through 618 or (resid 619 and (name N or name CA or name C or name O \ or name CB )) or resid 620 through 676 or resid 690 through 827 or resid 856 th \ rough 920 or (resid 921 and (name N or name CA or name C or name O or name CB )) \ or resid 922 through 1143 or (resid 1144 through 1146 and (name N or name CA or \ name C or name O or name CB )) or resid 1147 through 1305 or resid 1307)) selection = (chain 'B' and (resid 27 through 52 or (resid 53 and (name N or name CA or name \ C or name O or name CB )) or resid 54 through 66 or resid 82 through 95 or (resi \ d 96 through 97 and (name N or name CA or name C or name O or name CB )) or resi \ d 98 through 110 or (resid 111 and (name N or name CA or name C or name O or nam \ e CB )) or resid 112 or (resid 113 and (name N or name CA or name C or name O or \ name CB )) or resid 116 through 134 or (resid 135 through 138 and (name N or na \ me CA or name C or name O or name CB )) or resid 139 through 140 or resid 166 th \ rough 196 or resid 200 through 385 or (resid 386 and (name N or name CA or name \ C or name O or name CB )) or resid 387 through 470 or resid 491 through 613 or ( \ resid 614 and (name N or name CA or name C or name O or name CB )) or resid 615 \ through 618 or (resid 619 and (name N or name CA or name C or name O or name CB \ )) or resid 620 through 920 or (resid 921 and (name N or name CA or name C or na \ me O or name CB )) or resid 922 through 1141 or (resid 1142 and (name N or name \ CA or name C or name O or name CB )) or resid 1143 or (resid 1144 through 1146 a \ nd (name N or name CA or name C or name O or name CB )) or resid 1147 through 13 \ 05 or resid 1307)) selection = (chain 'C' and (resid 27 through 52 or (resid 53 and (name N or name CA or name \ C or name O or name CB )) or resid 54 through 66 or resid 82 through 95 or (resi \ d 96 through 97 and (name N or name CA or name C or name O or name CB )) or resi \ d 98 through 109 or (resid 110 through 111 and (name N or name CA or name C or n \ ame O or name CB )) or resid 112 or (resid 113 and (name N or name CA or name C \ or name O or name CB )) or resid 116 through 123 or (resid 124 through 125 and ( \ name N or name CA or name C or name O or name CB )) or resid 126 through 131 or \ (resid 132 and (name N or name CA or name C or name O or name CB )) or resid 133 \ or (resid 134 through 138 and (name N or name CA or name C or name O or name CB \ )) or resid 139 through 140 or resid 166 through 171 or (resid 172 and (name N \ or name CA or name C or name O or name CB )) or resid 187 through 196 or resid 2 \ 00 through 263 or resid 265 through 385 or (resid 386 and (name N or name CA or \ name C or name O or name CB )) or resid 387 through 470 or resid 491 through 827 \ or resid 856 through 1141 or (resid 1142 and (name N or name CA or name C or na \ me O or name CB )) or resid 1143 through 1144 or (resid 1145 through 1146 and (n \ ame N or name CA or name C or name O or name CB )) or resid 1147 through 1305 or \ resid 1307)) } ncs_group { reference = chain 'D' selection = chain 'H' } ncs_group { reference = chain 'E' selection = chain 'L' } ncs_group { reference = chain 'F' selection = chain 'J' selection = chain 'K' selection = chain 'M' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'V' selection = chain 'W' selection = chain 'X' } ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'N' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.090 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: 0.460 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 27.250 Find NCS groups from input model: 0.840 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 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 : 0.004 0.094 28054 Z= 0.192 Angle : 0.776 16.218 38317 Z= 0.387 Chirality : 0.053 0.719 4567 Planarity : 0.005 0.103 4789 Dihedral : 12.832 89.582 9519 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 0.21 % Allowed : 4.26 % Favored : 95.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.66 (0.13), residues: 3342 helix: -1.82 (0.17), residues: 631 sheet: 0.17 (0.17), residues: 809 loop : -1.43 (0.12), residues: 1902 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.033 0.003 ARG A 34 TYR 0.017 0.001 TYR B1067 PHE 0.020 0.001 PHE B 377 TRP 0.025 0.001 TRP B 104 HIS 0.003 0.000 HIS B1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.19 (27959) covalent geometry : angle 0.71717 / 0.37 (38074) SS BOND : bond 0.00260 / 0.16 ( 39) SS BOND : angle 1.24796 / 0.80 ( 78) hydrogen bonds : bond 0.12990 / 8.41 ( 1029) hydrogen bonds : angle 6.99512 / 4.81 ( 2808) Misc. bond : bond 0.00009 / 0.00 ( 1) link_ALPHA1-3 : bond 0.00492 / 0.25 ( 2) link_ALPHA1-3 : angle 1.44432 / 0.79 ( 6) link_ALPHA1-6 : bond 0.00651 / 0.32 ( 2) link_ALPHA1-6 : angle 2.43713 / 1.51 ( 6) link_BETA1-4 : bond 0.00874 / 0.50 ( 22) link_BETA1-4 : angle 3.71222 / 2.32 ( 66) link_BETA1-6 : bond 0.03131 / 1.50 ( 2) link_BETA1-6 : angle 5.83380 / 3.34 ( 6) link_NAG-ASN : bond 0.00853 / 0.45 ( 27) link_NAG-ASN : angle 5.22724 / 3.31 ( 81) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6684 Ramachandran restraints generated. 3342 Oldfield, 0 Emsley, 3342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6684 Ramachandran restraints generated. 3342 Oldfield, 0 Emsley, 3342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 485 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 479 time to evaluate : 0.945 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 582 LEU cc_start: 0.7589 (mt) cc_final: 0.7075 (pp) REVERT: A 754 LEU cc_start: 0.9044 (pp) cc_final: 0.8807 (tp) REVERT: A 948 LEU cc_start: 0.7921 (pp) cc_final: 0.7595 (pp) REVERT: A 974 SER cc_start: 0.9351 (t) cc_final: 0.8898 (m) REVERT: A 1002 GLN cc_start: 0.7684 (pt0) cc_final: 0.7137 (pt0) REVERT: B 338 PHE cc_start: 0.8322 (OUTLIER) cc_final: 0.7309 (t80) REVERT: B 347 PHE cc_start: 0.5450 (t80) cc_final: 0.4994 (m-80) REVERT: B 753 LEU cc_start: 0.8700 (tt) cc_final: 0.8447 (tt) REVERT: C 338 PHE cc_start: 0.8677 (OUTLIER) cc_final: 0.7807 (t80) REVERT: C 456 PHE cc_start: 0.8018 (m-80) cc_final: 0.7754 (m-80) REVERT: C 533 LEU cc_start: 0.8640 (mt) cc_final: 0.8192 (tt) REVERT: C 663 ASP cc_start: 0.7824 (t0) cc_final: 0.7513 (m-30) REVERT: E 35 TRP cc_start: 0.7788 (m100) cc_final: 0.7496 (m100) REVERT: H 58 ASN cc_start: 0.6211 (m-40) cc_final: 0.5899 (m-40) REVERT: L 58 ILE cc_start: 0.8140 (mm) cc_final: 0.7861 (mm) outliers start: 6 outliers final: 2 residues processed: 485 average time/residue: 0.1763 time to fit residues: 137.2296 Evaluate side-chains 243 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 239 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 488 CYS Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain C residue 338 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 197 optimal weight: 0.6980 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 0.2980 chunk 261 optimal weight: 0.4980 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 0.7980 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 9.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 207 HIS B 271 GLN ** B 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN C 314 GLN C 709 ASN L 6 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.161286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.124085 restraints weight = 41396.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.125311 restraints weight = 96751.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.126876 restraints weight = 60089.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.127016 restraints weight = 41691.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.128321 restraints weight = 32998.908| |-----------------------------------------------------------------------------| r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.1680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 28054 Z= 0.139 Angle : 0.709 16.764 38317 Z= 0.345 Chirality : 0.048 0.403 4567 Planarity : 0.004 0.052 4789 Dihedral : 5.176 58.022 3641 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 1.68 % Allowed : 8.96 % Favored : 89.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.67 (0.13), residues: 3342 helix: 0.04 (0.20), residues: 663 sheet: 0.51 (0.17), residues: 805 loop : -1.06 (0.13), residues: 1874 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 328 TYR 0.020 0.001 TYR B 91 PHE 0.028 0.002 PHE H 78 TRP 0.014 0.001 TRP B 436 HIS 0.003 0.001 HIS B 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.14 (27959) covalent geometry : angle 0.65668 / 0.33 (38074) SS BOND : bond 0.00431 / 0.23 ( 39) SS BOND : angle 2.35569 / 1.59 ( 78) hydrogen bonds : bond 0.04554 / 2.96 ( 1029) hydrogen bonds : angle 5.68840 / 3.92 ( 2808) Misc. bond : bond 0.00076 / 0.04 ( 1) link_ALPHA1-3 : bond 0.00671 / 0.35 ( 2) link_ALPHA1-3 : angle 1.60079 / 0.89 ( 6) link_ALPHA1-6 : bond 0.00889 / 0.46 ( 2) link_ALPHA1-6 : angle 1.73500 / 1.05 ( 6) link_BETA1-4 : bond 0.00965 / 0.57 ( 22) link_BETA1-4 : angle 3.07259 / 1.91 ( 66) link_BETA1-6 : bond 0.03386 / 1.61 ( 2) link_BETA1-6 : angle 3.78830 / 2.25 ( 6) link_NAG-ASN : bond 0.00707 / 0.38 ( 27) link_NAG-ASN : angle 4.51495 / 2.90 ( 81) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6684 Ramachandran restraints generated. 3342 Oldfield, 0 Emsley, 3342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6684 Ramachandran restraints generated. 3342 Oldfield, 0 Emsley, 3342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 277 time to evaluate : 1.093 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 582 LEU cc_start: 0.7551 (mt) cc_final: 0.7064 (pp) REVERT: A 606 ASN cc_start: 0.8171 (p0) cc_final: 0.7697 (p0) REVERT: A 692 ILE cc_start: 0.8696 (mt) cc_final: 0.8397 (mm) REVERT: A 974 SER cc_start: 0.9194 (t) cc_final: 0.8937 (m) REVERT: A 1002 GLN cc_start: 0.7619 (pt0) cc_final: 0.7262 (pt0) REVERT: B 201 PHE cc_start: 0.8035 (t80) cc_final: 0.7760 (t80) REVERT: B 338 PHE cc_start: 0.8379 (OUTLIER) cc_final: 0.7312 (t80) REVERT: B 347 PHE cc_start: 0.5724 (t80) cc_final: 0.5311 (m-80) REVERT: C 338 PHE cc_start: 0.8914 (OUTLIER) cc_final: 0.7616 (t80) REVERT: C 406 GLU cc_start: 0.8016 (mt-10) cc_final: 0.7642 (mt-10) REVERT: C 429 PHE cc_start: 0.9397 (t80) cc_final: 0.9007 (t80) REVERT: C 453 TYR cc_start: 0.8359 (p90) cc_final: 0.8043 (p90) REVERT: C 533 LEU cc_start: 0.8630 (mt) cc_final: 0.8252 (tt) REVERT: C 663 ASP cc_start: 0.8006 (t0) cc_final: 0.7636 (m-30) REVERT: L 58 ILE cc_start: 0.8086 (mm) cc_final: 0.7842 (mm) outliers start: 49 outliers final: 30 residues processed: 312 average time/residue: 0.1617 time to fit residues: 84.0705 Evaluate side-chains 252 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 220 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 343 ASN Chi-restraints excluded: chain B residue 467 ASP Chi-restraints excluded: chain B residue 488 CYS Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 749 CYS Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 338 PHE Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 110 ILE Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 90 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 282 optimal weight: 1.9990 chunk 176 optimal weight: 2.9990 chunk 85 optimal weight: 0.9990 chunk 121 optimal weight: 0.0010 chunk 86 optimal weight: 0.5980 chunk 72 optimal weight: 0.3980 chunk 34 optimal weight: 20.0000 chunk 187 optimal weight: 0.6980 chunk 298 optimal weight: 9.9990 chunk 73 optimal weight: 1.9990 chunk 127 optimal weight: 5.9990 overall best weight: 0.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 914 ASN B 207 HIS ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 58 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.162043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.125397 restraints weight = 41084.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.126609 restraints weight = 85966.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.127775 restraints weight = 63810.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.127822 restraints weight = 44629.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.128973 restraints weight = 35817.424| |-----------------------------------------------------------------------------| r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.2115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 28054 Z= 0.118 Angle : 0.642 16.564 38317 Z= 0.307 Chirality : 0.046 0.351 4567 Planarity : 0.004 0.039 4789 Dihedral : 4.872 55.244 3641 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.16 % Allowed : 9.20 % Favored : 88.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.14), residues: 3342 helix: 0.85 (0.21), residues: 651 sheet: 0.64 (0.18), residues: 784 loop : -0.96 (0.13), residues: 1907 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1107 TYR 0.015 0.001 TYR A1067 PHE 0.022 0.001 PHE H 78 TRP 0.013 0.001 TRP B 436 HIS 0.003 0.001 HIS B 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.12 (27959) covalent geometry : angle 0.59787 / 0.30 (38074) SS BOND : bond 0.00658 / 0.34 ( 39) SS BOND : angle 1.47935 / 0.98 ( 78) hydrogen bonds : bond 0.04147 / 2.70 ( 1029) hydrogen bonds : angle 5.27930 / 3.62 ( 2808) Misc. bond : bond 0.00046 / 0.02 ( 1) link_ALPHA1-3 : bond 0.00597 / 0.31 ( 2) link_ALPHA1-3 : angle 1.48639 / 0.81 ( 6) link_ALPHA1-6 : bond 0.00791 / 0.40 ( 2) link_ALPHA1-6 : angle 1.70779 / 1.06 ( 6) link_BETA1-4 : bond 0.00910 / 0.54 ( 22) link_BETA1-4 : angle 2.99979 / 1.86 ( 66) link_BETA1-6 : bond 0.02181 / 1.04 ( 2) link_BETA1-6 : angle 3.12300 / 1.85 ( 6) link_NAG-ASN : bond 0.00785 / 0.44 ( 27) link_NAG-ASN : angle 4.05529 / 2.64 ( 81) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6684 Ramachandran restraints generated. 3342 Oldfield, 0 Emsley, 3342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6684 Ramachandran restraints generated. 3342 Oldfield, 0 Emsley, 3342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 246 time to evaluate : 1.086 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 582 LEU cc_start: 0.7555 (mt) cc_final: 0.7032 (pp) REVERT: A 606 ASN cc_start: 0.8225 (p0) cc_final: 0.7725 (p0) REVERT: A 692 ILE cc_start: 0.8681 (mt) cc_final: 0.8369 (mm) REVERT: A 754 LEU cc_start: 0.9103 (pp) cc_final: 0.8753 (tp) REVERT: A 974 SER cc_start: 0.9152 (t) cc_final: 0.8940 (m) REVERT: A 1050 MET cc_start: 0.8283 (ptm) cc_final: 0.8075 (ptt) REVERT: B 201 PHE cc_start: 0.7980 (t80) cc_final: 0.7774 (t80) REVERT: B 338 PHE cc_start: 0.8440 (OUTLIER) cc_final: 0.7411 (t80) REVERT: B 347 PHE cc_start: 0.5786 (OUTLIER) cc_final: 0.5362 (m-80) REVERT: C 338 PHE cc_start: 0.8978 (OUTLIER) cc_final: 0.7592 (t80) REVERT: C 403 ARG cc_start: 0.7498 (ttm170) cc_final: 0.7078 (ttm-80) REVERT: C 453 TYR cc_start: 0.8432 (p90) cc_final: 0.8136 (p90) REVERT: C 533 LEU cc_start: 0.8614 (mt) cc_final: 0.8245 (tt) REVERT: C 663 ASP cc_start: 0.8078 (t0) cc_final: 0.7759 (m-30) REVERT: D 109 GLU cc_start: 0.8212 (tm-30) cc_final: 0.7737 (tm-30) REVERT: H 18 LEU cc_start: 0.6936 (pp) cc_final: 0.6628 (pp) REVERT: H 60 ASN cc_start: 0.8153 (t0) cc_final: 0.7847 (t0) REVERT: L 46 LEU cc_start: 0.8445 (tp) cc_final: 0.8223 (tt) REVERT: L 47 LEU cc_start: 0.7120 (OUTLIER) cc_final: 0.6622 (mt) REVERT: L 58 ILE cc_start: 0.8056 (mm) cc_final: 0.7774 (mm) REVERT: L 94 TRP cc_start: 0.6969 (t-100) cc_final: 0.5943 (t60) outliers start: 63 outliers final: 39 residues processed: 291 average time/residue: 0.1626 time to fit residues: 79.3403 Evaluate side-chains 258 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 215 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 467 ASP Chi-restraints excluded: chain B residue 488 CYS Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 749 CYS Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 338 PHE Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain D residue 54 SER Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 110 ILE Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 90 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 196 optimal weight: 5.9990 chunk 257 optimal weight: 0.9980 chunk 186 optimal weight: 2.9990 chunk 295 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 130 optimal weight: 5.9990 chunk 38 optimal weight: 9.9990 chunk 212 optimal weight: 7.9990 chunk 129 optimal weight: 6.9990 chunk 99 optimal weight: 0.8980 chunk 123 optimal weight: 2.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 498 GLN ** A 655 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS B 394 ASN B 655 HIS B 801 ASN B 913 GLN B1002 GLN C 957 GLN D 32 HIS L 6 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.153147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.116031 restraints weight = 41114.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.118551 restraints weight = 100796.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.118919 restraints weight = 43446.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.119137 restraints weight = 34752.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.119843 restraints weight = 28767.262| |-----------------------------------------------------------------------------| r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.2946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 28054 Z= 0.231 Angle : 0.771 14.710 38317 Z= 0.382 Chirality : 0.050 0.399 4567 Planarity : 0.005 0.070 4789 Dihedral : 5.359 54.976 3641 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.95 % Allowed : 10.37 % Favored : 86.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.70 (0.14), residues: 3342 helix: 0.39 (0.20), residues: 668 sheet: 0.68 (0.17), residues: 796 loop : -1.34 (0.13), residues: 1878 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A1107 TYR 0.025 0.002 TYR C 204 PHE 0.030 0.003 PHE A 92 TRP 0.023 0.002 TRP B 436 HIS 0.006 0.002 HIS A1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00560 / 0.23 (27959) covalent geometry : angle 0.73100 / 0.37 (38074) SS BOND : bond 0.00687 / 0.39 ( 39) SS BOND : angle 2.00737 / 1.31 ( 78) hydrogen bonds : bond 0.06436 / 4.23 ( 1029) hydrogen bonds : angle 5.61349 / 3.85 ( 2808) Misc. bond : bond 0.00030 / 0.02 ( 1) link_ALPHA1-3 : bond 0.00489 / 0.26 ( 2) link_ALPHA1-3 : angle 1.59850 / 0.85 ( 6) link_ALPHA1-6 : bond 0.00732 / 0.38 ( 2) link_ALPHA1-6 : angle 1.81529 / 1.09 ( 6) link_BETA1-4 : bond 0.00815 / 0.51 ( 22) link_BETA1-4 : angle 2.95315 / 1.84 ( 66) link_BETA1-6 : bond 0.02189 / 1.04 ( 2) link_BETA1-6 : angle 2.83078 / 1.65 ( 6) link_NAG-ASN : bond 0.00624 / 0.33 ( 27) link_NAG-ASN : angle 4.22807 / 2.78 ( 81) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6684 Ramachandran restraints generated. 3342 Oldfield, 0 Emsley, 3342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6684 Ramachandran restraints generated. 3342 Oldfield, 0 Emsley, 3342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 235 time to evaluate : 0.974 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 582 LEU cc_start: 0.7724 (mt) cc_final: 0.7033 (pp) REVERT: A 675 GLN cc_start: 0.7824 (OUTLIER) cc_final: 0.7168 (tm-30) REVERT: A 754 LEU cc_start: 0.9003 (OUTLIER) cc_final: 0.8782 (tp) REVERT: A 900 MET cc_start: 0.8085 (mtt) cc_final: 0.7682 (mtt) REVERT: B 338 PHE cc_start: 0.8584 (OUTLIER) cc_final: 0.7555 (t80) REVERT: B 347 PHE cc_start: 0.6286 (t80) cc_final: 0.5351 (m-80) REVERT: C 403 ARG cc_start: 0.7725 (ttm170) cc_final: 0.6710 (ttm-80) REVERT: C 453 TYR cc_start: 0.8573 (p90) cc_final: 0.8291 (p90) REVERT: C 533 LEU cc_start: 0.8747 (mt) cc_final: 0.8282 (tt) REVERT: C 823 PHE cc_start: 0.7655 (m-80) cc_final: 0.7405 (m-80) REVERT: D 109 GLU cc_start: 0.8275 (tm-30) cc_final: 0.7772 (tm-30) REVERT: L 37 GLN cc_start: 0.7324 (tt0) cc_final: 0.7104 (tm-30) REVERT: L 47 LEU cc_start: 0.7302 (OUTLIER) cc_final: 0.7009 (mt) REVERT: L 58 ILE cc_start: 0.8081 (mm) cc_final: 0.7827 (mm) REVERT: L 91 TYR cc_start: 0.8511 (p90) cc_final: 0.8284 (p90) outliers start: 86 outliers final: 59 residues processed: 299 average time/residue: 0.1616 time to fit residues: 80.4941 Evaluate side-chains 273 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 210 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 467 ASP Chi-restraints excluded: chain B residue 488 CYS Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 749 CYS Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 196 ASN Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 54 SER Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 110 ILE Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 90 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 50 optimal weight: 0.3980 chunk 197 optimal weight: 2.9990 chunk 259 optimal weight: 0.5980 chunk 23 optimal weight: 5.9990 chunk 220 optimal weight: 0.0370 chunk 154 optimal weight: 2.9990 chunk 237 optimal weight: 0.7980 chunk 274 optimal weight: 0.9990 chunk 270 optimal weight: 0.9980 chunk 96 optimal weight: 3.9990 chunk 40 optimal weight: 10.0000 overall best weight: 0.5658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 394 ASN ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN L 6 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.156813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.119125 restraints weight = 40842.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.120140 restraints weight = 96078.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.122142 restraints weight = 62084.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.121860 restraints weight = 41894.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.123445 restraints weight = 33458.404| |-----------------------------------------------------------------------------| r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.2993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 28054 Z= 0.115 Angle : 0.642 13.288 38317 Z= 0.308 Chirality : 0.045 0.313 4567 Planarity : 0.004 0.059 4789 Dihedral : 4.831 54.032 3639 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.89 % Allowed : 12.33 % Favored : 85.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.34 (0.14), residues: 3342 helix: 1.02 (0.21), residues: 659 sheet: 0.77 (0.18), residues: 807 loop : -1.18 (0.13), residues: 1876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 237 TYR 0.017 0.001 TYR A1138 PHE 0.022 0.001 PHE B 201 TRP 0.017 0.001 TRP L 94 HIS 0.003 0.001 HIS B1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.11 (27959) covalent geometry : angle 0.60273 / 0.30 (38074) SS BOND : bond 0.00362 / 0.20 ( 39) SS BOND : angle 1.34577 / 0.87 ( 78) hydrogen bonds : bond 0.04534 / 2.95 ( 1029) hydrogen bonds : angle 5.15804 / 3.54 ( 2808) Misc. bond : bond 0.00029 / 0.02 ( 1) link_ALPHA1-3 : bond 0.00539 / 0.28 ( 2) link_ALPHA1-3 : angle 1.47125 / 0.76 ( 6) link_ALPHA1-6 : bond 0.00703 / 0.36 ( 2) link_ALPHA1-6 : angle 1.74069 / 1.09 ( 6) link_BETA1-4 : bond 0.00894 / 0.53 ( 22) link_BETA1-4 : angle 2.93164 / 1.82 ( 66) link_BETA1-6 : bond 0.02105 / 1.00 ( 2) link_BETA1-6 : angle 2.83647 / 1.66 ( 6) link_NAG-ASN : bond 0.00635 / 0.35 ( 27) link_NAG-ASN : angle 3.79533 / 2.48 ( 81) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6684 Ramachandran restraints generated. 3342 Oldfield, 0 Emsley, 3342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6684 Ramachandran restraints generated. 3342 Oldfield, 0 Emsley, 3342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 234 time to evaluate : 1.020 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 535 LYS cc_start: 0.8267 (mtmt) cc_final: 0.7733 (tmtt) REVERT: A 582 LEU cc_start: 0.7740 (mt) cc_final: 0.7077 (pp) REVERT: A 675 GLN cc_start: 0.7753 (OUTLIER) cc_final: 0.7117 (tm-30) REVERT: A 753 LEU cc_start: 0.8707 (tt) cc_final: 0.8379 (tp) REVERT: A 979 ASP cc_start: 0.8251 (t0) cc_final: 0.8014 (t0) REVERT: A 1050 MET cc_start: 0.8170 (ptm) cc_final: 0.7938 (ptt) REVERT: B 338 PHE cc_start: 0.8593 (OUTLIER) cc_final: 0.7528 (t80) REVERT: B 347 PHE cc_start: 0.6165 (OUTLIER) cc_final: 0.5260 (m-80) REVERT: B 913 GLN cc_start: 0.7514 (OUTLIER) cc_final: 0.6846 (pm20) REVERT: B 978 ASN cc_start: 0.8642 (t0) cc_final: 0.8417 (m110) REVERT: C 403 ARG cc_start: 0.7722 (ttm170) cc_final: 0.7385 (ttm-80) REVERT: C 420 ASP cc_start: 0.7839 (p0) cc_final: 0.7557 (p0) REVERT: C 453 TYR cc_start: 0.8530 (p90) cc_final: 0.8076 (p90) REVERT: C 533 LEU cc_start: 0.8681 (mt) cc_final: 0.8207 (tt) REVERT: C 900 MET cc_start: 0.7856 (mmm) cc_final: 0.7432 (mtt) REVERT: D 109 GLU cc_start: 0.8276 (tm-30) cc_final: 0.7809 (tm-30) REVERT: E 35 TRP cc_start: 0.7450 (m100) cc_final: 0.7112 (m100) REVERT: H 58 ASN cc_start: 0.7245 (t0) cc_final: 0.6526 (t0) REVERT: H 73 THR cc_start: 0.7193 (m) cc_final: 0.6704 (t) REVERT: L 37 GLN cc_start: 0.7249 (tt0) cc_final: 0.6902 (tm-30) REVERT: L 47 LEU cc_start: 0.7156 (OUTLIER) cc_final: 0.6779 (mt) REVERT: L 58 ILE cc_start: 0.8076 (mm) cc_final: 0.7790 (mm) REVERT: L 94 TRP cc_start: 0.6812 (t-100) cc_final: 0.5809 (t60) outliers start: 55 outliers final: 35 residues processed: 276 average time/residue: 0.1555 time to fit residues: 71.5020 Evaluate side-chains 254 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 214 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 343 ASN Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 488 CYS Chi-restraints excluded: chain B residue 749 CYS Chi-restraints excluded: chain B residue 913 GLN Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain D residue 54 SER Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 110 ILE Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 90 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 102 optimal weight: 8.9990 chunk 71 optimal weight: 2.9990 chunk 264 optimal weight: 4.9990 chunk 166 optimal weight: 3.9990 chunk 192 optimal weight: 0.9980 chunk 138 optimal weight: 5.9990 chunk 116 optimal weight: 6.9990 chunk 43 optimal weight: 6.9990 chunk 129 optimal weight: 7.9990 chunk 144 optimal weight: 0.6980 chunk 118 optimal weight: 2.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 655 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 487 ASN B 501 ASN B 764 ASN C 234 ASN ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN C1005 GLN H 77 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.150549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.114121 restraints weight = 41683.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.117416 restraints weight = 100500.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.116953 restraints weight = 41181.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.117445 restraints weight = 32626.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.117942 restraints weight = 27243.684| |-----------------------------------------------------------------------------| r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.3474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.069 28054 Z= 0.266 Angle : 0.778 14.439 38317 Z= 0.384 Chirality : 0.050 0.438 4567 Planarity : 0.005 0.071 4789 Dihedral : 5.268 54.974 3637 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 2.82 % Allowed : 12.67 % Favored : 84.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.84 (0.14), residues: 3342 helix: 0.44 (0.20), residues: 656 sheet: 0.46 (0.17), residues: 827 loop : -1.47 (0.13), residues: 1859 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 905 TYR 0.025 0.002 TYR C1007 PHE 0.030 0.003 PHE A1089 TRP 0.027 0.002 TRP C 64 HIS 0.008 0.002 HIS B1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00649 / 0.27 (27959) covalent geometry : angle 0.73900 / 0.37 (38074) SS BOND : bond 0.00900 / 0.47 ( 39) SS BOND : angle 2.18461 / 1.40 ( 78) hydrogen bonds : bond 0.06568 / 4.31 ( 1029) hydrogen bonds : angle 5.58371 / 3.83 ( 2808) Misc. bond : bond 0.00028 / 0.01 ( 1) link_ALPHA1-3 : bond 0.00440 / 0.23 ( 2) link_ALPHA1-3 : angle 1.64877 / 0.86 ( 6) link_ALPHA1-6 : bond 0.00706 / 0.36 ( 2) link_ALPHA1-6 : angle 1.83373 / 1.11 ( 6) link_BETA1-4 : bond 0.00837 / 0.54 ( 22) link_BETA1-4 : angle 2.91502 / 1.81 ( 66) link_BETA1-6 : bond 0.01890 / 0.90 ( 2) link_BETA1-6 : angle 2.64406 / 1.54 ( 6) link_NAG-ASN : bond 0.00537 / 0.29 ( 27) link_NAG-ASN : angle 4.11012 / 2.72 ( 81) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6684 Ramachandran restraints generated. 3342 Oldfield, 0 Emsley, 3342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6684 Ramachandran restraints generated. 3342 Oldfield, 0 Emsley, 3342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 219 time to evaluate : 1.041 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 582 LEU cc_start: 0.7800 (mt) cc_final: 0.7081 (pp) REVERT: A 900 MET cc_start: 0.8151 (mtt) cc_final: 0.7781 (mtt) REVERT: B 338 PHE cc_start: 0.8721 (OUTLIER) cc_final: 0.7678 (t80) REVERT: B 347 PHE cc_start: 0.6443 (t80) cc_final: 0.5362 (m-80) REVERT: B 913 GLN cc_start: 0.7950 (OUTLIER) cc_final: 0.7299 (pm20) REVERT: C 403 ARG cc_start: 0.7934 (ttm170) cc_final: 0.6844 (ttm-80) REVERT: C 420 ASP cc_start: 0.7878 (p0) cc_final: 0.7615 (p0) REVERT: C 453 TYR cc_start: 0.8554 (p90) cc_final: 0.8181 (p90) REVERT: C 533 LEU cc_start: 0.8775 (mt) cc_final: 0.8282 (tt) REVERT: D 95 CYS cc_start: 0.5245 (p) cc_final: 0.4724 (p) REVERT: D 108 PHE cc_start: 0.7504 (m-80) cc_final: 0.7264 (m-80) REVERT: D 109 GLU cc_start: 0.8252 (tm-30) cc_final: 0.7783 (tm-30) REVERT: E 35 TRP cc_start: 0.7592 (m100) cc_final: 0.7310 (m100) REVERT: H 58 ASN cc_start: 0.7249 (t0) cc_final: 0.6319 (t0) REVERT: L 47 LEU cc_start: 0.7307 (OUTLIER) cc_final: 0.7027 (mt) REVERT: L 58 ILE cc_start: 0.8081 (mm) cc_final: 0.7824 (mm) REVERT: L 94 TRP cc_start: 0.6813 (t-100) cc_final: 0.6591 (t-100) outliers start: 82 outliers final: 59 residues processed: 283 average time/residue: 0.1512 time to fit residues: 71.4009 Evaluate side-chains 271 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 209 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 343 ASN Chi-restraints excluded: chain B residue 519 HIS Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 749 CYS Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 913 GLN Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 54 SER Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain H residue 110 ILE Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 90 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 26 optimal weight: 9.9990 chunk 206 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 151 optimal weight: 2.9990 chunk 196 optimal weight: 4.9990 chunk 166 optimal weight: 0.9990 chunk 157 optimal weight: 0.5980 chunk 7 optimal weight: 0.1980 chunk 214 optimal weight: 0.6980 chunk 24 optimal weight: 6.9990 chunk 70 optimal weight: 0.8980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 907 ASN ** B 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.154459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.118613 restraints weight = 40589.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.121136 restraints weight = 97185.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.120964 restraints weight = 44151.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.121365 restraints weight = 34307.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.121820 restraints weight = 29490.264| |-----------------------------------------------------------------------------| r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.3459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 28054 Z= 0.124 Angle : 0.655 12.928 38317 Z= 0.316 Chirality : 0.046 0.304 4567 Planarity : 0.004 0.058 4789 Dihedral : 4.780 54.481 3636 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.61 % Allowed : 13.22 % Favored : 84.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.14), residues: 3342 helix: 0.99 (0.21), residues: 649 sheet: 0.56 (0.17), residues: 826 loop : -1.30 (0.13), residues: 1867 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 237 TYR 0.020 0.001 TYR A1138 PHE 0.023 0.001 PHE B 201 TRP 0.014 0.001 TRP B 104 HIS 0.003 0.000 HIS B1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 (27959) covalent geometry : angle 0.61569 / 0.31 (38074) SS BOND : bond 0.00399 / 0.22 ( 39) SS BOND : angle 1.63306 / 1.08 ( 78) hydrogen bonds : bond 0.04862 / 3.17 ( 1029) hydrogen bonds : angle 5.18414 / 3.55 ( 2808) Misc. bond : bond 0.00026 / 0.01 ( 1) link_ALPHA1-3 : bond 0.00519 / 0.26 ( 2) link_ALPHA1-3 : angle 1.47295 / 0.75 ( 6) link_ALPHA1-6 : bond 0.00649 / 0.33 ( 2) link_ALPHA1-6 : angle 1.77385 / 1.11 ( 6) link_BETA1-4 : bond 0.00905 / 0.54 ( 22) link_BETA1-4 : angle 2.90471 / 1.80 ( 66) link_BETA1-6 : bond 0.01903 / 0.91 ( 2) link_BETA1-6 : angle 2.60379 / 1.53 ( 6) link_NAG-ASN : bond 0.00595 / 0.32 ( 27) link_NAG-ASN : angle 3.80517 / 2.49 ( 81) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6684 Ramachandran restraints generated. 3342 Oldfield, 0 Emsley, 3342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6684 Ramachandran restraints generated. 3342 Oldfield, 0 Emsley, 3342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 217 time to evaluate : 1.054 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 582 LEU cc_start: 0.7771 (mt) cc_final: 0.7111 (pp) REVERT: A 675 GLN cc_start: 0.7799 (OUTLIER) cc_final: 0.7466 (tm-30) REVERT: A 900 MET cc_start: 0.7911 (mtt) cc_final: 0.7521 (mtt) REVERT: B 338 PHE cc_start: 0.8732 (OUTLIER) cc_final: 0.7746 (t80) REVERT: B 347 PHE cc_start: 0.6193 (t80) cc_final: 0.5212 (m-80) REVERT: B 564 GLN cc_start: 0.8943 (OUTLIER) cc_final: 0.8471 (mp10) REVERT: B 644 GLN cc_start: 0.6980 (OUTLIER) cc_final: 0.5406 (tm-30) REVERT: B 913 GLN cc_start: 0.7759 (OUTLIER) cc_final: 0.7111 (pm20) REVERT: C 403 ARG cc_start: 0.7838 (ttm170) cc_final: 0.6773 (ttm-80) REVERT: C 420 ASP cc_start: 0.7805 (p0) cc_final: 0.7568 (p0) REVERT: C 453 TYR cc_start: 0.8528 (p90) cc_final: 0.8105 (p90) REVERT: C 533 LEU cc_start: 0.8731 (mt) cc_final: 0.8233 (tt) REVERT: C 584 ILE cc_start: 0.8761 (OUTLIER) cc_final: 0.8535 (pt) REVERT: C 900 MET cc_start: 0.7965 (mmm) cc_final: 0.7403 (mtt) REVERT: D 95 CYS cc_start: 0.5266 (p) cc_final: 0.4770 (p) REVERT: D 99 VAL cc_start: 0.9487 (p) cc_final: 0.9279 (m) REVERT: D 109 GLU cc_start: 0.8239 (tm-30) cc_final: 0.7835 (tm-30) REVERT: E 35 TRP cc_start: 0.7544 (m100) cc_final: 0.7248 (m100) REVERT: H 58 ASN cc_start: 0.7154 (t0) cc_final: 0.6739 (t0) REVERT: L 47 LEU cc_start: 0.7162 (OUTLIER) cc_final: 0.6884 (mt) REVERT: L 58 ILE cc_start: 0.8053 (mm) cc_final: 0.7804 (mm) REVERT: L 94 TRP cc_start: 0.6540 (t-100) cc_final: 0.5697 (t60) outliers start: 76 outliers final: 56 residues processed: 280 average time/residue: 0.1604 time to fit residues: 74.9699 Evaluate side-chains 272 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 209 time to evaluate : 1.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 907 ASN Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 343 ASN Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 488 CYS Chi-restraints excluded: chain B residue 519 HIS Chi-restraints excluded: chain B residue 564 GLN Chi-restraints excluded: chain B residue 644 GLN Chi-restraints excluded: chain B residue 749 CYS Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 913 GLN Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain D residue 54 SER Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain H residue 110 ILE Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 90 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 138 optimal weight: 0.5980 chunk 71 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 111 optimal weight: 5.9990 chunk 216 optimal weight: 1.9990 chunk 175 optimal weight: 5.9990 chunk 17 optimal weight: 1.9990 chunk 313 optimal weight: 9.9990 chunk 319 optimal weight: 1.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 422 ASN ** B 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 907 ASN C1002 GLN E 92 ASN L 6 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.151537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.116908 restraints weight = 41505.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.119696 restraints weight = 99297.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.118505 restraints weight = 40403.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.119236 restraints weight = 32677.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.119566 restraints weight = 26120.110| |-----------------------------------------------------------------------------| r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.3707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 28054 Z= 0.203 Angle : 0.723 13.702 38317 Z= 0.353 Chirality : 0.048 0.387 4567 Planarity : 0.005 0.063 4789 Dihedral : 4.984 54.878 3636 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.76 % Favored : 95.21 % Rotamer: Outliers : 2.58 % Allowed : 13.91 % Favored : 83.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.80 (0.14), residues: 3342 helix: 0.72 (0.21), residues: 648 sheet: 0.38 (0.18), residues: 806 loop : -1.45 (0.13), residues: 1888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 66 TYR 0.021 0.002 TYR C1067 PHE 0.026 0.002 PHE B1121 TRP 0.021 0.002 TRP C 64 HIS 0.006 0.001 HIS B1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00489 / 0.20 (27959) covalent geometry : angle 0.68388 / 0.34 (38074) SS BOND : bond 0.00569 / 0.32 ( 39) SS BOND : angle 2.12031 / 1.41 ( 78) hydrogen bonds : bond 0.05892 / 3.86 ( 1029) hydrogen bonds : angle 5.36428 / 3.67 ( 2808) Misc. bond : bond 0.00026 / 0.01 ( 1) link_ALPHA1-3 : bond 0.00457 / 0.24 ( 2) link_ALPHA1-3 : angle 1.55804 / 0.80 ( 6) link_ALPHA1-6 : bond 0.00669 / 0.34 ( 2) link_ALPHA1-6 : angle 1.79463 / 1.09 ( 6) link_BETA1-4 : bond 0.00836 / 0.53 ( 22) link_BETA1-4 : angle 2.86552 / 1.79 ( 66) link_BETA1-6 : bond 0.01603 / 0.76 ( 2) link_BETA1-6 : angle 2.36551 / 1.39 ( 6) link_NAG-ASN : bond 0.00521 / 0.28 ( 27) link_NAG-ASN : angle 3.90639 / 2.57 ( 81) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6684 Ramachandran restraints generated. 3342 Oldfield, 0 Emsley, 3342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6684 Ramachandran restraints generated. 3342 Oldfield, 0 Emsley, 3342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 209 time to evaluate : 1.059 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 582 LEU cc_start: 0.7788 (mt) cc_final: 0.7057 (pp) REVERT: A 900 MET cc_start: 0.8076 (mtt) cc_final: 0.7701 (mtt) REVERT: B 338 PHE cc_start: 0.8760 (OUTLIER) cc_final: 0.7749 (t80) REVERT: B 347 PHE cc_start: 0.6480 (t80) cc_final: 0.5328 (m-80) REVERT: B 644 GLN cc_start: 0.7466 (OUTLIER) cc_final: 0.5956 (tm-30) REVERT: B 913 GLN cc_start: 0.7914 (OUTLIER) cc_final: 0.7233 (pm20) REVERT: C 403 ARG cc_start: 0.7882 (ttm170) cc_final: 0.6843 (ttm-80) REVERT: C 420 ASP cc_start: 0.7815 (p0) cc_final: 0.7589 (p0) REVERT: C 453 TYR cc_start: 0.8576 (p90) cc_final: 0.8197 (p90) REVERT: C 533 LEU cc_start: 0.8753 (mt) cc_final: 0.8247 (tt) REVERT: C 584 ILE cc_start: 0.8823 (OUTLIER) cc_final: 0.8583 (pt) REVERT: C 900 MET cc_start: 0.8175 (mmm) cc_final: 0.7526 (mtt) REVERT: D 95 CYS cc_start: 0.5399 (p) cc_final: 0.4866 (p) REVERT: D 99 VAL cc_start: 0.9535 (p) cc_final: 0.9332 (m) REVERT: D 109 GLU cc_start: 0.8230 (tm-30) cc_final: 0.7854 (tm-30) REVERT: E 35 TRP cc_start: 0.7570 (m100) cc_final: 0.7288 (m100) REVERT: H 58 ASN cc_start: 0.7223 (t0) cc_final: 0.6899 (t0) REVERT: L 35 TRP cc_start: 0.8194 (m100) cc_final: 0.7914 (m100) REVERT: L 47 LEU cc_start: 0.7246 (OUTLIER) cc_final: 0.6969 (mt) REVERT: L 58 ILE cc_start: 0.8081 (mm) cc_final: 0.7861 (mm) REVERT: L 94 TRP cc_start: 0.6587 (t-100) cc_final: 0.5840 (t60) outliers start: 75 outliers final: 59 residues processed: 269 average time/residue: 0.1618 time to fit residues: 73.2758 Evaluate side-chains 266 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 202 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 343 ASN Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 488 CYS Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 519 HIS Chi-restraints excluded: chain B residue 644 GLN Chi-restraints excluded: chain B residue 749 CYS Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 913 GLN Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 907 ASN Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain D residue 54 SER Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain H residue 110 ILE Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 90 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 30 optimal weight: 8.9990 chunk 237 optimal weight: 6.9990 chunk 53 optimal weight: 5.9990 chunk 74 optimal weight: 1.9990 chunk 245 optimal weight: 0.2980 chunk 297 optimal weight: 6.9990 chunk 167 optimal weight: 0.0770 chunk 298 optimal weight: 10.0000 chunk 324 optimal weight: 3.9990 chunk 162 optimal weight: 0.5980 chunk 278 optimal weight: 2.9990 overall best weight: 1.1942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 907 ASN ** B 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN E 92 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.152960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.116942 restraints weight = 40887.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.119065 restraints weight = 99257.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.119603 restraints weight = 49466.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.120076 restraints weight = 35013.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.120831 restraints weight = 29840.567| |-----------------------------------------------------------------------------| r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.3763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 28054 Z= 0.155 Angle : 0.676 13.655 38317 Z= 0.327 Chirality : 0.046 0.321 4567 Planarity : 0.004 0.054 4789 Dihedral : 4.819 54.773 3636 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.34 % Allowed : 14.29 % Favored : 83.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.70 (0.14), residues: 3342 helix: 0.92 (0.21), residues: 655 sheet: 0.45 (0.18), residues: 799 loop : -1.44 (0.13), residues: 1888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 66 TYR 0.021 0.001 TYR A1138 PHE 0.024 0.002 PHE B 201 TRP 0.013 0.001 TRP B 886 HIS 0.003 0.001 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.15 (27959) covalent geometry : angle 0.63774 / 0.32 (38074) SS BOND : bond 0.00458 / 0.26 ( 39) SS BOND : angle 1.82467 / 1.21 ( 78) hydrogen bonds : bond 0.05176 / 3.39 ( 1029) hydrogen bonds : angle 5.21829 / 3.56 ( 2808) Misc. bond : bond 0.00025 / 0.01 ( 1) link_ALPHA1-3 : bond 0.00509 / 0.26 ( 2) link_ALPHA1-3 : angle 1.49916 / 0.77 ( 6) link_ALPHA1-6 : bond 0.00633 / 0.32 ( 2) link_ALPHA1-6 : angle 1.76957 / 1.10 ( 6) link_BETA1-4 : bond 0.00865 / 0.52 ( 22) link_BETA1-4 : angle 2.86067 / 1.78 ( 66) link_BETA1-6 : bond 0.01142 / 0.54 ( 2) link_BETA1-6 : angle 2.05320 / 1.20 ( 6) link_NAG-ASN : bond 0.00540 / 0.28 ( 27) link_NAG-ASN : angle 3.76555 / 2.46 ( 81) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6684 Ramachandran restraints generated. 3342 Oldfield, 0 Emsley, 3342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6684 Ramachandran restraints generated. 3342 Oldfield, 0 Emsley, 3342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 207 time to evaluate : 1.048 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 582 LEU cc_start: 0.7762 (mt) cc_final: 0.7086 (pp) REVERT: A 900 MET cc_start: 0.8046 (mtt) cc_final: 0.7654 (mtt) REVERT: B 65 PHE cc_start: 0.7438 (m-10) cc_final: 0.7225 (m-10) REVERT: B 338 PHE cc_start: 0.8762 (OUTLIER) cc_final: 0.7765 (t80) REVERT: B 347 PHE cc_start: 0.6225 (t80) cc_final: 0.5104 (m-80) REVERT: B 644 GLN cc_start: 0.7386 (OUTLIER) cc_final: 0.5926 (tm-30) REVERT: B 913 GLN cc_start: 0.7884 (OUTLIER) cc_final: 0.7276 (pm20) REVERT: C 403 ARG cc_start: 0.7860 (ttm170) cc_final: 0.6777 (ttm-80) REVERT: C 420 ASP cc_start: 0.7796 (p0) cc_final: 0.7574 (p0) REVERT: C 453 TYR cc_start: 0.8548 (p90) cc_final: 0.8068 (p90) REVERT: C 533 LEU cc_start: 0.8752 (mt) cc_final: 0.8241 (tt) REVERT: C 568 ASP cc_start: 0.6463 (m-30) cc_final: 0.5895 (p0) REVERT: C 584 ILE cc_start: 0.8780 (OUTLIER) cc_final: 0.8562 (pt) REVERT: C 900 MET cc_start: 0.8100 (mmm) cc_final: 0.7488 (mtt) REVERT: C 985 ASP cc_start: 0.6695 (OUTLIER) cc_final: 0.6261 (m-30) REVERT: D 95 CYS cc_start: 0.5414 (p) cc_final: 0.4807 (p) REVERT: D 99 VAL cc_start: 0.9490 (p) cc_final: 0.9267 (m) REVERT: D 108 PHE cc_start: 0.7382 (m-80) cc_final: 0.7104 (m-80) REVERT: D 109 GLU cc_start: 0.8238 (tm-30) cc_final: 0.7821 (tm-30) REVERT: E 35 TRP cc_start: 0.7546 (m100) cc_final: 0.7246 (m100) REVERT: E 42 GLN cc_start: 0.6310 (mm-40) cc_final: 0.6072 (mm-40) REVERT: H 58 ASN cc_start: 0.7141 (t0) cc_final: 0.6756 (t0) REVERT: L 35 TRP cc_start: 0.8245 (m100) cc_final: 0.8019 (m100) REVERT: L 47 LEU cc_start: 0.7188 (OUTLIER) cc_final: 0.6749 (mt) REVERT: L 94 TRP cc_start: 0.6579 (t-100) cc_final: 0.5811 (t60) outliers start: 68 outliers final: 58 residues processed: 263 average time/residue: 0.1659 time to fit residues: 72.8405 Evaluate side-chains 265 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 201 time to evaluate : 1.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 907 ASN Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 343 ASN Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 488 CYS Chi-restraints excluded: chain B residue 519 HIS Chi-restraints excluded: chain B residue 644 GLN Chi-restraints excluded: chain B residue 749 CYS Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 913 GLN Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain D residue 54 SER Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 110 ILE Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 90 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 243 optimal weight: 1.9990 chunk 203 optimal weight: 5.9990 chunk 173 optimal weight: 0.8980 chunk 210 optimal weight: 0.5980 chunk 24 optimal weight: 20.0000 chunk 194 optimal weight: 0.7980 chunk 204 optimal weight: 3.9990 chunk 268 optimal weight: 0.7980 chunk 75 optimal weight: 0.5980 chunk 327 optimal weight: 5.9990 chunk 240 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 907 ASN ** B 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN E 92 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.154007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.117790 restraints weight = 40965.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.119954 restraints weight = 99687.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.120544 restraints weight = 49267.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.120797 restraints weight = 35655.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.121741 restraints weight = 30013.446| |-----------------------------------------------------------------------------| r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.3790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 28054 Z= 0.125 Angle : 0.647 13.272 38317 Z= 0.311 Chirality : 0.045 0.299 4567 Planarity : 0.004 0.048 4789 Dihedral : 4.654 54.733 3636 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 2.27 % Allowed : 14.22 % Favored : 83.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.56 (0.14), residues: 3342 helix: 1.10 (0.21), residues: 655 sheet: 0.48 (0.18), residues: 818 loop : -1.37 (0.13), residues: 1869 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 237 TYR 0.019 0.001 TYR A1138 PHE 0.025 0.001 PHE B 201 TRP 0.014 0.001 TRP B 104 HIS 0.004 0.001 HIS B1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 (27959) covalent geometry : angle 0.61152 / 0.30 (38074) SS BOND : bond 0.00399 / 0.23 ( 39) SS BOND : angle 1.55898 / 1.04 ( 78) hydrogen bonds : bond 0.04715 / 3.09 ( 1029) hydrogen bonds : angle 5.07909 / 3.46 ( 2808) Misc. bond : bond 0.00026 / 0.01 ( 1) link_ALPHA1-3 : bond 0.00534 / 0.27 ( 2) link_ALPHA1-3 : angle 1.47830 / 0.75 ( 6) link_ALPHA1-6 : bond 0.00634 / 0.32 ( 2) link_ALPHA1-6 : angle 1.71693 / 1.07 ( 6) link_BETA1-4 : bond 0.00876 / 0.52 ( 22) link_BETA1-4 : angle 2.80653 / 1.75 ( 66) link_BETA1-6 : bond 0.00945 / 0.45 ( 2) link_BETA1-6 : angle 1.54203 / 0.85 ( 6) link_NAG-ASN : bond 0.00554 / 0.29 ( 27) link_NAG-ASN : angle 3.62941 / 2.37 ( 81) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6684 Ramachandran restraints generated. 3342 Oldfield, 0 Emsley, 3342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6684 Ramachandran restraints generated. 3342 Oldfield, 0 Emsley, 3342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 213 time to evaluate : 1.014 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 582 LEU cc_start: 0.7710 (mt) cc_final: 0.7025 (pp) REVERT: A 675 GLN cc_start: 0.7795 (OUTLIER) cc_final: 0.7514 (tm-30) REVERT: A 900 MET cc_start: 0.7885 (mtt) cc_final: 0.7510 (mtt) REVERT: B 338 PHE cc_start: 0.8753 (OUTLIER) cc_final: 0.7767 (t80) REVERT: B 347 PHE cc_start: 0.6142 (t80) cc_final: 0.5086 (m-80) REVERT: B 564 GLN cc_start: 0.8917 (OUTLIER) cc_final: 0.8443 (mp10) REVERT: B 644 GLN cc_start: 0.7337 (OUTLIER) cc_final: 0.5901 (tm-30) REVERT: B 913 GLN cc_start: 0.7809 (OUTLIER) cc_final: 0.7184 (pm20) REVERT: C 403 ARG cc_start: 0.7808 (ttm170) cc_final: 0.6722 (ttm-80) REVERT: C 420 ASP cc_start: 0.7786 (p0) cc_final: 0.7563 (p0) REVERT: C 453 TYR cc_start: 0.8534 (p90) cc_final: 0.8093 (p90) REVERT: C 533 LEU cc_start: 0.8728 (mt) cc_final: 0.8226 (tt) REVERT: C 568 ASP cc_start: 0.6419 (m-30) cc_final: 0.6032 (p0) REVERT: C 584 ILE cc_start: 0.8777 (OUTLIER) cc_final: 0.8552 (pt) REVERT: C 900 MET cc_start: 0.8009 (mmm) cc_final: 0.7378 (mtt) REVERT: D 95 CYS cc_start: 0.5440 (p) cc_final: 0.4830 (p) REVERT: D 99 VAL cc_start: 0.9479 (p) cc_final: 0.9268 (m) REVERT: D 108 PHE cc_start: 0.7399 (m-80) cc_final: 0.7119 (m-80) REVERT: D 109 GLU cc_start: 0.8192 (tm-30) cc_final: 0.7786 (tm-30) REVERT: E 11 LEU cc_start: 0.7812 (mt) cc_final: 0.7524 (tt) REVERT: E 35 TRP cc_start: 0.7517 (m100) cc_final: 0.7249 (m100) REVERT: E 42 GLN cc_start: 0.6070 (mm-40) cc_final: 0.5834 (mm-40) REVERT: H 58 ASN cc_start: 0.7077 (t0) cc_final: 0.6620 (t0) REVERT: L 35 TRP cc_start: 0.8308 (m100) cc_final: 0.8060 (m100) REVERT: L 47 LEU cc_start: 0.7242 (OUTLIER) cc_final: 0.6795 (mt) REVERT: L 94 TRP cc_start: 0.6522 (t-100) cc_final: 0.5752 (t60) outliers start: 66 outliers final: 52 residues processed: 266 average time/residue: 0.1630 time to fit residues: 72.7303 Evaluate side-chains 265 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 206 time to evaluate : 1.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 907 ASN Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 343 ASN Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 488 CYS Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 519 HIS Chi-restraints excluded: chain B residue 564 GLN Chi-restraints excluded: chain B residue 644 GLN Chi-restraints excluded: chain B residue 749 CYS Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 913 GLN Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain D residue 54 SER Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain H residue 110 ILE Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 90 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 134 optimal weight: 0.5980 chunk 295 optimal weight: 7.9990 chunk 264 optimal weight: 3.9990 chunk 78 optimal weight: 1.9990 chunk 274 optimal weight: 0.8980 chunk 178 optimal weight: 4.9990 chunk 159 optimal weight: 0.9980 chunk 73 optimal weight: 0.8980 chunk 299 optimal weight: 0.9990 chunk 63 optimal weight: 2.9990 chunk 115 optimal weight: 0.3980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 907 ASN ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.154360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.117777 restraints weight = 40528.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.119592 restraints weight = 98331.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.120554 restraints weight = 52540.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.120982 restraints weight = 36096.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.121791 restraints weight = 31090.932| |-----------------------------------------------------------------------------| r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.3834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 28054 Z= 0.125 Angle : 0.644 15.055 38317 Z= 0.308 Chirality : 0.045 0.295 4567 Planarity : 0.004 0.048 4789 Dihedral : 4.579 54.528 3636 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 2.23 % Allowed : 14.35 % Favored : 83.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.50 (0.14), residues: 3342 helix: 1.16 (0.21), residues: 655 sheet: 0.52 (0.18), residues: 823 loop : -1.33 (0.13), residues: 1864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 237 TYR 0.028 0.001 TYR H 52 PHE 0.027 0.001 PHE A 906 TRP 0.013 0.001 TRP B 104 HIS 0.004 0.001 HIS B1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.12 (27959) covalent geometry : angle 0.60831 / 0.30 (38074) SS BOND : bond 0.00391 / 0.22 ( 39) SS BOND : angle 1.58536 / 1.06 ( 78) hydrogen bonds : bond 0.04569 / 2.99 ( 1029) hydrogen bonds : angle 5.02277 / 3.42 ( 2808) Misc. bond : bond 0.00025 / 0.01 ( 1) link_ALPHA1-3 : bond 0.00527 / 0.27 ( 2) link_ALPHA1-3 : angle 1.47966 / 0.75 ( 6) link_ALPHA1-6 : bond 0.00623 / 0.32 ( 2) link_ALPHA1-6 : angle 1.69564 / 1.05 ( 6) link_BETA1-4 : bond 0.00863 / 0.52 ( 22) link_BETA1-4 : angle 2.77548 / 1.73 ( 66) link_BETA1-6 : bond 0.00950 / 0.45 ( 2) link_BETA1-6 : angle 1.47213 / 0.81 ( 6) link_NAG-ASN : bond 0.00537 / 0.28 ( 27) link_NAG-ASN : angle 3.57476 / 2.33 ( 81) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3648.15 seconds wall clock time: 64 minutes 23.47 seconds (3863.47 seconds total)