Starting phenix.real_space_refine on Sat Jun 6 15:42:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9z1m_73749/06_2026/9z1m_73749.cif Found real_map, /net/cci-nas-00/data/ceres_data/9z1m_73749/06_2026/9z1m_73749.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9z1m_73749/06_2026/9z1m_73749.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9z1m_73749/06_2026/9z1m_73749.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9z1m_73749/06_2026/9z1m_73749.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9z1m_73749/06_2026/9z1m_73749.map" } resolution = 3.06 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= 0.012 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 126 5.16 5 C 18301 2.51 5 N 4754 2.21 5 O 5569 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 28750 Number of models: 1 Model: "" Number of chains: 19 Chain: "D" Number of atoms: 952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 952 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 3, 'TRANS': 122} Chain: "E" Number of atoms: 952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 952 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 3, 'TRANS': 122} Chain: "F" Number of atoms: 952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 952 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 3, 'TRANS': 122} Chain: "B" Number of atoms: 8510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1085, 8510 Classifications: {'peptide': 1085} Link IDs: {'PTRANS': 57, 'TRANS': 1027} Chain breaks: 2 Chain: "C" Number of atoms: 8510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1085, 8510 Classifications: {'peptide': 1085} Link IDs: {'PTRANS': 57, 'TRANS': 1027} Chain breaks: 2 Chain: "A" Number of atoms: 8510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1085, 8510 Classifications: {'peptide': 1085} Link IDs: {'PTRANS': 57, 'TRANS': 1027} Chain breaks: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 7.87, per 1000 atoms: 0.27 Number of scatterers: 28750 At special positions: 0 Unit cell: (149.621, 152.277, 232.843, 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 126 16.00 O 5569 8.00 N 4754 7.00 C 18301 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=35, symmetry=0 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 50 " - pdb=" SG CYS D 104 " distance=2.02 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 50 " - pdb=" SG CYS E 104 " distance=2.02 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.03 Simple disulfide: pdb=" SG CYS F 50 " - pdb=" SG CYS F 104 " distance=2.03 Simple disulfide: pdb=" SG CYS B 288 " - pdb=" SG CYS B 298 " distance=2.03 Simple disulfide: pdb=" SG CYS B 333 " - pdb=" SG CYS B 358 " distance=2.03 Simple disulfide: pdb=" SG CYS B 376 " - pdb=" SG CYS B 429 " distance=2.03 Simple disulfide: pdb=" SG CYS B 388 " - pdb=" SG CYS B 521 " distance=2.03 Simple disulfide: pdb=" SG CYS B 477 " - pdb=" SG CYS B 484 " distance=2.03 Simple disulfide: pdb=" SG CYS B 534 " - pdb=" SG CYS B 586 " distance=2.03 Simple disulfide: pdb=" SG CYS B 613 " - pdb=" SG CYS B 645 " distance=2.03 Simple disulfide: pdb=" SG CYS B 658 " - pdb=" SG CYS B 667 " distance=2.03 Simple disulfide: pdb=" SG CYS B 734 " - pdb=" SG CYS B 756 " distance=2.03 Simple disulfide: pdb=" SG CYS B 739 " - pdb=" SG CYS B 745 " distance=2.03 Simple disulfide: pdb=" SG CYS B1028 " - pdb=" SG CYS B1039 " distance=2.03 Simple disulfide: pdb=" SG CYS C 288 " - pdb=" SG CYS C 298 " distance=2.03 Simple disulfide: pdb=" SG CYS C 333 " - pdb=" SG CYS C 358 " distance=2.02 Simple disulfide: pdb=" SG CYS C 376 " - pdb=" SG CYS C 429 " distance=2.03 Simple disulfide: pdb=" SG CYS C 388 " - pdb=" SG CYS C 521 " distance=2.03 Simple disulfide: pdb=" SG CYS C 477 " - pdb=" SG CYS C 484 " distance=2.03 Simple disulfide: pdb=" SG CYS C 613 " - pdb=" SG CYS C 645 " distance=2.02 Simple disulfide: pdb=" SG CYS C 658 " - pdb=" SG CYS C 667 " distance=2.03 Simple disulfide: pdb=" SG CYS C 734 " - pdb=" SG CYS C 756 " distance=2.03 Simple disulfide: pdb=" SG CYS C 739 " - pdb=" SG CYS C 745 " distance=2.03 Simple disulfide: pdb=" SG CYS C1028 " - pdb=" SG CYS C1039 " distance=2.03 Simple disulfide: pdb=" SG CYS A 288 " - pdb=" SG CYS A 298 " distance=2.03 Simple disulfide: pdb=" SG CYS A 333 " - pdb=" SG CYS A 358 " distance=2.03 Simple disulfide: pdb=" SG CYS A 376 " - pdb=" SG CYS A 429 " distance=2.03 Simple disulfide: pdb=" SG CYS A 388 " - pdb=" SG CYS A 521 " distance=2.03 Simple disulfide: pdb=" SG CYS A 477 " - pdb=" SG CYS A 484 " distance=2.03 Simple disulfide: pdb=" SG CYS A 613 " - pdb=" SG CYS A 645 " distance=2.02 Simple disulfide: pdb=" SG CYS A 658 " - pdb=" SG CYS A 667 " distance=2.03 Simple disulfide: pdb=" SG CYS A1028 " - pdb=" SG CYS A1039 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " NAG-ASN " NAG B1301 " - " ASN B 612 " " NAG B1302 " - " ASN B 705 " " NAG C1301 " - " ASN C 705 " " NAG C1302 " - " ASN C1130 " " NAG G 1 " - " ASN B 797 " " NAG H 1 " - " ASN B 713 " " NAG I 1 " - " ASN B1094 " " NAG J 1 " - " ASN B1130 " " NAG K 1 " - " ASN C 713 " " NAG L 1 " - " ASN C 797 " " NAG M 1 " - " ASN C1094 " " NAG N 1 " - " ASN A 713 " " NAG O 1 " - " ASN A 797 " " NAG P 1 " - " ASN A1094 " " NAG Q 1 " - " ASN A1130 " Time building additional restraints: 2.58 Conformation dependent library (CDL) restraints added in 1.8 seconds 7218 Ramachandran restraints generated. 3609 Oldfield, 0 Emsley, 3609 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6744 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 52 sheets defined 21.0% alpha, 23.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.16 Creating SS restraints... Processing helix chain 'D' and resid 87 through 91 removed outlier: 4.134A pdb=" N THR D 91 " --> pdb=" O LEU D 88 " (cutoff:3.500A) Processing helix chain 'F' and resid 87 through 91 Processing helix chain 'B' and resid 291 through 301 Processing helix chain 'B' and resid 334 through 340 removed outlier: 4.069A pdb=" N VAL B 338 " --> pdb=" O PRO B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 367 removed outlier: 3.671A pdb=" N TYR B 366 " --> pdb=" O TYR B 362 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ASN B 367 " --> pdb=" O SER B 363 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 362 through 367' Processing helix chain 'B' and resid 612 through 622 removed outlier: 3.729A pdb=" N VAL B 616 " --> pdb=" O ASN B 612 " (cutoff:3.500A) Processing helix chain 'B' and resid 733 through 739 Processing helix chain 'B' and resid 743 through 750 removed outlier: 3.603A pdb=" N LEU B 748 " --> pdb=" O GLU B 744 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU B 750 " --> pdb=" O SER B 746 " (cutoff:3.500A) Processing helix chain 'B' and resid 751 through 753 No H-bonds generated for 'chain 'B' and resid 751 through 753' Processing helix chain 'B' and resid 754 through 779 removed outlier: 3.919A pdb=" N GLN B 758 " --> pdb=" O SER B 754 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU B 763 " --> pdb=" O LEU B 759 " (cutoff:3.500A) Processing helix chain 'B' and resid 812 through 822 removed outlier: 3.577A pdb=" N VAL B 822 " --> pdb=" O LEU B 818 " (cutoff:3.500A) Processing helix chain 'B' and resid 862 through 880 Processing helix chain 'B' and resid 882 through 886 Processing helix chain 'B' and resid 893 through 905 Processing helix chain 'B' and resid 909 through 914 removed outlier: 4.320A pdb=" N TYR B 913 " --> pdb=" O GLN B 909 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLU B 914 " --> pdb=" O ASN B 910 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 909 through 914' Processing helix chain 'B' and resid 915 through 937 Processing helix chain 'B' and resid 941 through 961 removed outlier: 3.709A pdb=" N GLN B 945 " --> pdb=" O LEU B 941 " (cutoff:3.500A) Processing helix chain 'B' and resid 962 through 964 No H-bonds generated for 'chain 'B' and resid 962 through 964' Processing helix chain 'B' and resid 972 through 980 removed outlier: 3.542A pdb=" N ILE B 976 " --> pdb=" O VAL B 972 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LEU B 980 " --> pdb=" O ILE B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 981 through 1029 removed outlier: 4.700A pdb=" N VAL B 987 " --> pdb=" O PRO B 983 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N ARG B 991 " --> pdb=" O VAL B 987 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N LEU B 992 " --> pdb=" O GLN B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1137 through 1145 Processing helix chain 'C' and resid 291 through 300 Processing helix chain 'C' and resid 335 through 340 Processing helix chain 'C' and resid 380 through 384 removed outlier: 4.206A pdb=" N LEU C 384 " --> pdb=" O PRO C 381 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 404 No H-bonds generated for 'chain 'C' and resid 402 through 404' Processing helix chain 'C' and resid 413 through 419 Processing helix chain 'C' and resid 612 through 622 Processing helix chain 'C' and resid 733 through 739 Processing helix chain 'C' and resid 742 through 750 Processing helix chain 'C' and resid 751 through 753 No H-bonds generated for 'chain 'C' and resid 751 through 753' Processing helix chain 'C' and resid 754 through 778 removed outlier: 3.595A pdb=" N GLN C 758 " --> pdb=" O SER C 754 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N THR C 774 " --> pdb=" O GLN C 770 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLN C 775 " --> pdb=" O ASP C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 812 through 822 removed outlier: 3.704A pdb=" N VAL C 822 " --> pdb=" O LEU C 818 " (cutoff:3.500A) Processing helix chain 'C' and resid 862 through 880 Processing helix chain 'C' and resid 882 through 886 Processing helix chain 'C' and resid 893 through 905 removed outlier: 3.741A pdb=" N ILE C 905 " --> pdb=" O ARG C 901 " (cutoff:3.500A) Processing helix chain 'C' and resid 909 through 915 removed outlier: 3.694A pdb=" N TYR C 913 " --> pdb=" O GLN C 909 " (cutoff:3.500A) Processing helix chain 'C' and resid 915 through 937 removed outlier: 3.620A pdb=" N ILE C 930 " --> pdb=" O ALA C 926 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N GLN C 931 " --> pdb=" O ILE C 927 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ASP C 932 " --> pdb=" O GLY C 928 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU C 934 " --> pdb=" O ILE C 930 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N PHE C 935 " --> pdb=" O GLN C 931 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N THR C 937 " --> pdb=" O SER C 933 " (cutoff:3.500A) Processing helix chain 'C' and resid 941 through 961 removed outlier: 3.628A pdb=" N GLN C 945 " --> pdb=" O LEU C 941 " (cutoff:3.500A) Processing helix chain 'C' and resid 962 through 964 No H-bonds generated for 'chain 'C' and resid 962 through 964' Processing helix chain 'C' and resid 972 through 979 removed outlier: 3.758A pdb=" N ILE C 976 " --> pdb=" O VAL C 972 " (cutoff:3.500A) Processing helix chain 'C' and resid 981 through 984 Processing helix chain 'C' and resid 985 through 1029 removed outlier: 4.656A pdb=" N ARG C 991 " --> pdb=" O VAL C 987 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N LEU C 992 " --> pdb=" O GLN C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1137 through 1146 removed outlier: 3.541A pdb=" N GLU C1146 " --> pdb=" O ASP C1142 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 300 Processing helix chain 'A' and resid 334 through 340 Processing helix chain 'A' and resid 383 through 387 removed outlier: 3.508A pdb=" N ASP A 386 " --> pdb=" O LYS A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 407 removed outlier: 5.399A pdb=" N SER A 405 " --> pdb=" O ASN A 402 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE A 407 " --> pdb=" O VAL A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 418 removed outlier: 3.545A pdb=" N TYR A 418 " --> pdb=" O ASN A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 613 through 623 removed outlier: 3.951A pdb=" N VAL A 618 " --> pdb=" O THR A 614 " (cutoff:3.500A) Processing helix chain 'A' and resid 733 through 739 Processing helix chain 'A' and resid 742 through 750 Processing helix chain 'A' and resid 754 through 779 removed outlier: 4.158A pdb=" N GLN A 758 " --> pdb=" O SER A 754 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N LEU A 759 " --> pdb=" O PHE A 755 " (cutoff:3.500A) Processing helix chain 'A' and resid 812 through 822 removed outlier: 3.508A pdb=" N VAL A 822 " --> pdb=" O LEU A 818 " (cutoff:3.500A) Processing helix chain 'A' and resid 862 through 880 Processing helix chain 'A' and resid 882 through 886 Processing helix chain 'A' and resid 893 through 904 Processing helix chain 'A' and resid 909 through 914 removed outlier: 3.742A pdb=" N TYR A 913 " --> pdb=" O GLN A 909 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLU A 914 " --> pdb=" O ASN A 910 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 909 through 914' Processing helix chain 'A' and resid 915 through 937 removed outlier: 3.592A pdb=" N LEU A 934 " --> pdb=" O ILE A 930 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N PHE A 935 " --> pdb=" O GLN A 931 " (cutoff:3.500A) Processing helix chain 'A' and resid 941 through 961 removed outlier: 3.706A pdb=" N GLN A 945 " --> pdb=" O LEU A 941 " (cutoff:3.500A) Processing helix chain 'A' and resid 962 through 964 No H-bonds generated for 'chain 'A' and resid 962 through 964' Processing helix chain 'A' and resid 972 through 978 Processing helix chain 'A' and resid 981 through 1029 removed outlier: 4.524A pdb=" N VAL A 987 " --> pdb=" O PRO A 983 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N ARG A 991 " --> pdb=" O VAL A 987 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N LEU A 992 " --> pdb=" O GLN A 988 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL A1029 " --> pdb=" O MET A1025 " (cutoff:3.500A) Processing helix chain 'A' and resid 1135 through 1142 removed outlier: 3.584A pdb=" N LEU A1139 " --> pdb=" O ASP A1135 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLU A1140 " --> pdb=" O PRO A1136 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 5 through 7 removed outlier: 3.748A pdb=" N LEU D 18 " --> pdb=" O MET D 83 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 10 through 12 removed outlier: 4.055A pdb=" N GLY D 10 " --> pdb=" O GLN D 124 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N THR D 126 " --> pdb=" O GLY D 10 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL D 12 " --> pdb=" O THR D 126 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N THR D 123 " --> pdb=" O TYR D 94 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL D 93 " --> pdb=" O GLN D 39 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N THR D 34 " --> pdb=" O CYS D 50 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N CYS D 50 " --> pdb=" O THR D 34 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 10 through 12 removed outlier: 4.055A pdb=" N GLY D 10 " --> pdb=" O GLN D 124 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N THR D 126 " --> pdb=" O GLY D 10 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL D 12 " --> pdb=" O THR D 126 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N THR D 123 " --> pdb=" O TYR D 94 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 6 through 7 removed outlier: 3.609A pdb=" N LEU E 18 " --> pdb=" O MET E 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 6 through 7 Processing sheet with id=AA6, first strand: chain 'E' and resid 10 through 12 removed outlier: 5.884A pdb=" N GLY E 10 " --> pdb=" O THR E 126 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N THR E 123 " --> pdb=" O TYR E 94 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL E 93 " --> pdb=" O GLN E 39 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ALA E 33 " --> pdb=" O ASP E 99 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 5 through 7 removed outlier: 3.598A pdb=" N LEU F 20 " --> pdb=" O LEU F 81 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N THR F 78 " --> pdb=" O ASP F 73 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ASP F 73 " --> pdb=" O THR F 78 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N TYR F 80 " --> pdb=" O SER F 71 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N THR F 69 " --> pdb=" O GLN F 82 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 46 through 51 removed outlier: 6.503A pdb=" N TRP F 36 " --> pdb=" O VAL F 48 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N CYS F 50 " --> pdb=" O THR F 34 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N THR F 34 " --> pdb=" O CYS F 50 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N TYR F 94 " --> pdb=" O THR F 123 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR F 123 " --> pdb=" O TYR F 94 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 29 through 32 removed outlier: 3.534A pdb=" N SER B 32 " --> pdb=" O SER B 61 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N SER B 61 " --> pdb=" O SER B 32 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N ASN B 62 " --> pdb=" O TYR B 266 " (cutoff:3.500A) removed outlier: 5.344A pdb=" N TYR B 266 " --> pdb=" O ASN B 62 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LYS B 185 " --> pdb=" O ILE B 208 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLU B 189 " --> pdb=" O LYS B 204 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N TYR B 202 " --> pdb=" O VAL B 191 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N PHE B 199 " --> pdb=" O ASP B 225 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N ASP B 225 " --> pdb=" O PHE B 199 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N ILE B 201 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N HIS B 205 " --> pdb=" O ALA B 219 " (cutoff:3.500A) removed outlier: 9.701A pdb=" N ALA B 219 " --> pdb=" O HIS B 205 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N VAL B 37 " --> pdb=" O LEU B 220 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 43 through 44 removed outlier: 3.907A pdb=" N ALA C 571 " --> pdb=" O GLY C 562 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N PHE C 539 " --> pdb=" O LEU C 542 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N GLU C 321 " --> pdb=" O ASN C 536 " (cutoff:3.500A) removed outlier: 8.911A pdb=" N ASN C 538 " --> pdb=" O GLU C 321 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 49 through 56 removed outlier: 4.088A pdb=" N ASP B 284 " --> pdb=" O LYS B 275 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 82 through 83 removed outlier: 3.524A pdb=" N ARG B 234 " --> pdb=" O GLY B 106 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N VAL B 125 " --> pdb=" O SER B 170 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N SER B 170 " --> pdb=" O VAL B 125 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 308 through 316 removed outlier: 6.836A pdb=" N VAL B 591 " --> pdb=" O THR B 312 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N ASN B 314 " --> pdb=" O GLY B 589 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N GLY B 589 " --> pdb=" O ASN B 314 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N GLY B 590 " --> pdb=" O GLN B 609 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 351 through 355 removed outlier: 3.817A pdb=" N ASN B 351 " --> pdb=" O SER B 396 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N SER B 396 " --> pdb=" O ASN B 351 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE B 355 " --> pdb=" O VAL B 392 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N VAL B 392 " --> pdb=" O ILE B 355 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 388 through 389 Processing sheet with id=AB7, first strand: chain 'B' and resid 449 through 451 Processing sheet with id=AB8, first strand: chain 'B' and resid 470 through 471 Processing sheet with id=AB9, first strand: chain 'B' and resid 534 through 539 removed outlier: 5.019A pdb=" N ASP B 570 " --> pdb=" O ILE B 583 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ALA B 571 " --> pdb=" O GLY B 562 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N PHE B 561 " --> pdb=" O PHE A 44 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 650 through 656 removed outlier: 6.129A pdb=" N GLU B 650 " --> pdb=" O ALA B 690 " (cutoff:3.500A) removed outlier: 8.738A pdb=" N THR B 692 " --> pdb=" O GLU B 650 " (cutoff:3.500A) removed outlier: 8.848A pdb=" N VAL B 652 " --> pdb=" O THR B 692 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N ILE B 666 " --> pdb=" O ILE B 662 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 697 through 698 removed outlier: 6.879A pdb=" N ALA B 697 " --> pdb=" O ILE A 784 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'B' and resid 707 through 711 removed outlier: 3.510A pdb=" N THR B1072 " --> pdb=" O SER B1093 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ALA B1074 " --> pdb=" O PHE B1091 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N PHE B1091 " --> pdb=" O ALA B1074 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 714 through 724 removed outlier: 7.353A pdb=" N GLY B1055 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N SER B1051 " --> pdb=" O GLY B1055 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N VAL B1057 " --> pdb=" O PRO B1049 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N LEU B1059 " --> pdb=" O SER B1047 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N SER B1047 " --> pdb=" O LEU B1059 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N VAL B1061 " --> pdb=" O LEU B1045 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 729 through 732 removed outlier: 4.474A pdb=" N LYS B 729 " --> pdb=" O LEU B 857 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 783 through 784 Processing sheet with id=AC7, first strand: chain 'B' and resid 1116 through 1118 Processing sheet with id=AC8, first strand: chain 'C' and resid 221 through 227 removed outlier: 7.076A pdb=" N ILE C 201 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N ASP C 225 " --> pdb=" O PHE C 199 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N PHE C 199 " --> pdb=" O ASP C 225 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LYS C 193 " --> pdb=" O LYS C 200 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N TYR C 202 " --> pdb=" O VAL C 191 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LYS C 204 " --> pdb=" O GLU C 189 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N GLU C 189 " --> pdb=" O LYS C 204 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N THR C 206 " --> pdb=" O LEU C 187 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LYS C 185 " --> pdb=" O ILE C 208 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N TYR C 266 " --> pdb=" O ASN C 62 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N ASN C 62 " --> pdb=" O TYR C 266 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N SER C 61 " --> pdb=" O SER C 32 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N SER C 32 " --> pdb=" O SER C 61 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N SER C 28 " --> pdb=" O TRP C 65 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N GLN C 27 " --> pdb=" O GLY C 254 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 43 through 44 removed outlier: 4.383A pdb=" N ALA A 571 " --> pdb=" O GLY A 562 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N ASP A 570 " --> pdb=" O ILE A 583 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 49 through 56 removed outlier: 3.878A pdb=" N ASP C 284 " --> pdb=" O LYS C 275 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 165 through 170 removed outlier: 5.145A pdb=" N PHE C 166 " --> pdb=" O VAL C 129 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N VAL C 129 " --> pdb=" O PHE C 166 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LYS C 128 " --> pdb=" O LEU C 117 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N GLY C 102 " --> pdb=" O LEU C 238 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 308 through 315 removed outlier: 7.087A pdb=" N VAL C 591 " --> pdb=" O THR C 312 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N ASN C 314 " --> pdb=" O GLY C 589 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N GLY C 589 " --> pdb=" O ASN C 314 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N GLY C 590 " --> pdb=" O GLN C 609 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 353 through 355 removed outlier: 3.589A pdb=" N THR C 353 " --> pdb=" O ALA C 394 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N VAL C 392 " --> pdb=" O ILE C 355 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 353 through 355 removed outlier: 3.589A pdb=" N THR C 353 " --> pdb=" O ALA C 394 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N VAL C 392 " --> pdb=" O ILE C 355 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 449 through 451 Processing sheet with id=AD7, first strand: chain 'C' and resid 650 through 651 removed outlier: 5.956A pdb=" N GLU C 650 " --> pdb=" O ALA C 690 " (cutoff:3.500A) removed outlier: 8.528A pdb=" N THR C 692 " --> pdb=" O GLU C 650 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N SER C 687 " --> pdb=" O GLN C 671 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLN C 671 " --> pdb=" O SER C 687 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 707 through 711 removed outlier: 3.800A pdb=" N ALA C1074 " --> pdb=" O PHE C1091 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N PHE C1091 " --> pdb=" O ALA C1074 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 714 through 724 removed outlier: 7.299A pdb=" N GLY C1055 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 5.614A pdb=" N SER C1051 " --> pdb=" O GLY C1055 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N VAL C1057 " --> pdb=" O PRO C1049 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N LEU C1059 " --> pdb=" O SER C1047 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N SER C1047 " --> pdb=" O LEU C1059 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N VAL C1061 " --> pdb=" O LEU C1045 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 729 through 732 removed outlier: 4.436A pdb=" N LYS C 729 " --> pdb=" O LEU C 857 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 783 through 784 Processing sheet with id=AE3, first strand: chain 'C' and resid 1116 through 1118 Processing sheet with id=AE4, first strand: chain 'A' and resid 29 through 32 removed outlier: 3.993A pdb=" N SER A 61 " --> pdb=" O SER A 32 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'A' and resid 37 through 38 removed outlier: 7.030A pdb=" N VAL A 37 " --> pdb=" O LEU A 220 " (cutoff:3.500A) removed outlier: 9.384A pdb=" N LEU A 220 " --> pdb=" O HIS A 205 " (cutoff:3.500A) removed outlier: 9.195A pdb=" N HIS A 205 " --> pdb=" O LEU A 220 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N SER A 203 " --> pdb=" O PRO A 222 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL A 224 " --> pdb=" O ILE A 201 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'A' and resid 50 through 56 Processing sheet with id=AE7, first strand: chain 'A' and resid 167 through 170 removed outlier: 3.527A pdb=" N SER A 170 " --> pdb=" O VAL A 125 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N VAL A 125 " --> pdb=" O SER A 170 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHE A 126 " --> pdb=" O VAL A 119 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N VAL A 119 " --> pdb=" O PHE A 126 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ASN A 120 " --> pdb=" O ARG A 101 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N ARG A 101 " --> pdb=" O ASN A 120 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N GLY A 102 " --> pdb=" O LEU A 238 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'A' and resid 308 through 315 removed outlier: 7.045A pdb=" N VAL A 591 " --> pdb=" O THR A 312 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N ASN A 314 " --> pdb=" O GLY A 589 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N GLY A 589 " --> pdb=" O ASN A 314 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N GLY A 590 " --> pdb=" O GLN A 609 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'A' and resid 353 through 355 removed outlier: 4.002A pdb=" N THR A 353 " --> pdb=" O ALA A 394 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA A 394 " --> pdb=" O THR A 353 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL A 392 " --> pdb=" O ILE A 355 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N LYS A 375 " --> pdb=" O VAL A 430 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'A' and resid 399 through 400 Processing sheet with id=AF2, first strand: chain 'A' and resid 449 through 451 Processing sheet with id=AF3, first strand: chain 'A' and resid 650 through 656 removed outlier: 6.118A pdb=" N GLU A 650 " --> pdb=" O ALA A 690 " (cutoff:3.500A) removed outlier: 8.710A pdb=" N THR A 692 " --> pdb=" O GLU A 650 " (cutoff:3.500A) removed outlier: 9.021A pdb=" N VAL A 652 " --> pdb=" O THR A 692 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'A' and resid 708 through 724 removed outlier: 6.412A pdb=" N GLN A1067 " --> pdb=" O THR A 712 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N PHE A 714 " --> pdb=" O PRO A1065 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N ILE A 716 " --> pdb=" O TYR A1063 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N TYR A1063 " --> pdb=" O ILE A 716 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N VAL A 718 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N VAL A1061 " --> pdb=" O VAL A 718 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N THR A 720 " --> pdb=" O LEU A1059 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N LEU A1059 " --> pdb=" O THR A 720 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N ILE A 722 " --> pdb=" O VAL A1057 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N VAL A1057 " --> pdb=" O ILE A 722 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N GLY A1055 " --> pdb=" O PRO A 724 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N TYR A1063 " --> pdb=" O HIS A1044 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N HIS A1044 " --> pdb=" O TYR A1063 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'A' and resid 729 through 732 removed outlier: 4.253A pdb=" N LYS A 729 " --> pdb=" O LEU A 857 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'A' and resid 1116 through 1118 Processing sheet with id=AF7, first strand: chain 'A' and resid 1090 through 1093 removed outlier: 3.503A pdb=" N VAL A1090 " --> pdb=" O THR A1101 " (cutoff:3.500A) 967 hydrogen bonds defined for protein. 2664 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: 7.55 Time building geometry restraints manager: 3.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8955 1.34 - 1.46: 7268 1.46 - 1.58: 13058 1.58 - 1.71: 0 1.71 - 1.83: 159 Bond restraints: 29440 Sorted by residual: bond pdb=" C1 NAG L 2 " pdb=" O5 NAG L 2 " ideal model delta sigma weight residual 1.406 1.470 -0.064 2.00e-02 2.50e+03 1.01e+01 bond pdb=" N SER E 52 " pdb=" CA SER E 52 " ideal model delta sigma weight residual 1.452 1.487 -0.035 1.25e-02 6.40e+03 7.71e+00 bond pdb=" C PHE C 213 " pdb=" N PRO C 214 " ideal model delta sigma weight residual 1.332 1.363 -0.031 1.12e-02 7.97e+03 7.64e+00 bond pdb=" C1 NAG J 2 " pdb=" O5 NAG J 2 " ideal model delta sigma weight residual 1.406 1.461 -0.055 2.00e-02 2.50e+03 7.43e+00 bond pdb=" C1 NAG P 2 " pdb=" O5 NAG P 2 " ideal model delta sigma weight residual 1.406 1.458 -0.052 2.00e-02 2.50e+03 6.66e+00 ... (remaining 29435 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.14: 39435 3.14 - 6.28: 528 6.28 - 9.42: 63 9.42 - 12.56: 13 12.56 - 15.71: 4 Bond angle restraints: 40043 Sorted by residual: angle pdb=" C THR E 112 " pdb=" N ASP E 113 " pdb=" CA ASP E 113 " ideal model delta sigma weight residual 121.54 135.86 -14.32 1.91e+00 2.74e-01 5.62e+01 angle pdb=" C SER B 742 " pdb=" N THR B 743 " pdb=" CA THR B 743 " ideal model delta sigma weight residual 121.54 133.36 -11.82 1.91e+00 2.74e-01 3.83e+01 angle pdb=" C ASP D 55 " pdb=" CA ASP D 55 " pdb=" CB ASP D 55 " ideal model delta sigma weight residual 116.54 109.97 6.57 1.15e+00 7.56e-01 3.26e+01 angle pdb=" N PRO C 982 " pdb=" CA PRO C 982 " pdb=" C PRO C 982 " ideal model delta sigma weight residual 110.70 117.52 -6.82 1.22e+00 6.72e-01 3.12e+01 angle pdb=" C LYS E 76 " pdb=" N ASN E 77 " pdb=" CA ASN E 77 " ideal model delta sigma weight residual 121.54 132.20 -10.66 1.91e+00 2.74e-01 3.11e+01 ... (remaining 40038 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 16195 17.90 - 35.80: 1302 35.80 - 53.69: 229 53.69 - 71.59: 60 71.59 - 89.49: 13 Dihedral angle restraints: 17799 sinusoidal: 7257 harmonic: 10542 Sorted by residual: dihedral pdb=" CB CYS A 333 " pdb=" SG CYS A 333 " pdb=" SG CYS A 358 " pdb=" CB CYS A 358 " ideal model delta sinusoidal sigma weight residual -86.00 -139.50 53.50 1 1.00e+01 1.00e-02 3.89e+01 dihedral pdb=" CB CYS B 739 " pdb=" SG CYS B 739 " pdb=" SG CYS B 745 " pdb=" CB CYS B 745 " ideal model delta sinusoidal sigma weight residual -86.00 -37.36 -48.64 1 1.00e+01 1.00e-02 3.26e+01 dihedral pdb=" CA GLY E 102 " pdb=" C GLY E 102 " pdb=" N VAL E 103 " pdb=" CA VAL E 103 " ideal model delta harmonic sigma weight residual -180.00 -152.29 -27.71 0 5.00e+00 4.00e-02 3.07e+01 ... (remaining 17796 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 3938 0.087 - 0.174: 541 0.174 - 0.260: 46 0.260 - 0.347: 10 0.347 - 0.434: 5 Chirality restraints: 4540 Sorted by residual: chirality pdb=" C1 NAG Q 1 " pdb=" ND2 ASN A1130 " pdb=" C2 NAG Q 1 " pdb=" O5 NAG Q 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.97 -0.43 2.00e-01 2.50e+01 4.71e+00 chirality pdb=" CB THR A 206 " pdb=" CA THR A 206 " pdb=" OG1 THR A 206 " pdb=" CG2 THR A 206 " both_signs ideal model delta sigma weight residual False 2.55 2.16 0.39 2.00e-01 2.50e+01 3.90e+00 chirality pdb=" C1 NAG J 1 " pdb=" ND2 ASN B1130 " pdb=" C2 NAG J 1 " pdb=" O5 NAG J 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.01 -0.39 2.00e-01 2.50e+01 3.87e+00 ... (remaining 4537 not shown) Planarity restraints: 5171 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TRP C 629 " 0.020 2.00e-02 2.50e+03 4.04e-02 1.63e+01 pdb=" C TRP C 629 " -0.070 2.00e-02 2.50e+03 pdb=" O TRP C 629 " 0.026 2.00e-02 2.50e+03 pdb=" N ARG C 630 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 38 " -0.044 2.00e-02 2.50e+03 2.83e-02 1.60e+01 pdb=" CG TYR B 38 " 0.064 2.00e-02 2.50e+03 pdb=" CD1 TYR B 38 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 TYR B 38 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR B 38 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR B 38 " -0.008 2.00e-02 2.50e+03 pdb=" CZ TYR B 38 " 0.007 2.00e-02 2.50e+03 pdb=" OH TYR B 38 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 422 " -0.060 5.00e-02 4.00e+02 9.22e-02 1.36e+01 pdb=" N PRO A 423 " 0.159 5.00e-02 4.00e+02 pdb=" CA PRO A 423 " -0.049 5.00e-02 4.00e+02 pdb=" CD PRO A 423 " -0.050 5.00e-02 4.00e+02 ... (remaining 5168 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 5932 2.78 - 3.31: 24382 3.31 - 3.84: 45764 3.84 - 4.37: 51052 4.37 - 4.90: 91047 Nonbonded interactions: 218177 Sorted by model distance: nonbonded pdb=" OG SER B 70 " pdb=" O ASN B 73 " model vdw 2.253 3.040 nonbonded pdb=" O ALA A 875 " pdb=" OG1 THR A 879 " model vdw 2.270 3.040 nonbonded pdb=" OG SER A 435 " pdb=" O PRO A 503 " model vdw 2.288 3.040 nonbonded pdb=" OG1 THR B1112 " pdb=" OD1 ASP B1114 " model vdw 2.304 3.040 nonbonded pdb=" O GLY E 102 " pdb=" OG SER E 106 " model vdw 2.305 3.040 ... (remaining 218172 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' selection = (chain 'B' and resid 26 through 1146) selection = (chain 'C' and resid 26 through 1146) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 12.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.050 Extract box with map and model: 0.650 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 31.420 Find NCS groups from input model: 0.710 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 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 : 0.005 0.081 29501 Z= 0.242 Angle : 0.938 15.706 40191 Z= 0.495 Chirality : 0.059 0.434 4540 Planarity : 0.007 0.092 5156 Dihedral : 13.321 89.490 10950 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.99 % Favored : 93.77 % Rotamer: Outliers : 0.03 % Allowed : 0.51 % Favored : 99.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.05 (0.13), residues: 3609 helix: -0.31 (0.18), residues: 653 sheet: -0.21 (0.18), residues: 791 loop : -2.26 (0.12), residues: 2165 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG B 630 TYR 0.064 0.002 TYR B 38 PHE 0.047 0.003 PHE B 213 TRP 0.053 0.003 TRP A1098 HIS 0.016 0.002 HIS F 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00534 / 0.24 (29440) covalent geometry : angle 0.92415 / 0.49 (40043) SS BOND : bond 0.00423 / 0.26 ( 35) SS BOND : angle 1.45535 / 0.96 ( 70) hydrogen bonds : bond 0.22127 / 14.71 ( 956) hydrogen bonds : angle 7.90180 / 5.42 ( 2664) link_BETA1-4 : bond 0.00594 / 0.34 ( 11) link_BETA1-4 : angle 2.76313 / 1.60 ( 33) link_NAG-ASN : bond 0.00937 / 0.62 ( 15) link_NAG-ASN : angle 4.04232 / 2.68 ( 45) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7218 Ramachandran restraints generated. 3609 Oldfield, 0 Emsley, 3609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7218 Ramachandran restraints generated. 3609 Oldfield, 0 Emsley, 3609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 3159 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 281 time to evaluate : 1.080 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 83 MET cc_start: 0.6061 (mpp) cc_final: 0.5648 (mmm) REVERT: E 114 ASP cc_start: 0.7974 (p0) cc_final: 0.7738 (p0) REVERT: B 87 ASP cc_start: 0.8008 (m-30) cc_final: 0.7611 (m-30) REVERT: C 175 MET cc_start: 0.5389 (mmp) cc_final: 0.5049 (ptt) REVERT: C 418 TYR cc_start: 0.6849 (m-80) cc_final: 0.6482 (m-80) REVERT: C 438 LEU cc_start: 0.9051 (mp) cc_final: 0.8847 (tt) REVERT: C 504 TYR cc_start: 0.8626 (m-80) cc_final: 0.8389 (m-10) REVERT: A 402 ASN cc_start: 0.8293 (t0) cc_final: 0.7868 (m-40) REVERT: A 981 ASP cc_start: 0.8636 (m-30) cc_final: 0.8094 (m-30) REVERT: A 984 GLU cc_start: 0.9068 (mp0) cc_final: 0.8788 (pm20) REVERT: A 990 ASP cc_start: 0.8323 (p0) cc_final: 0.7819 (t70) outliers start: 1 outliers final: 0 residues processed: 281 average time/residue: 0.1779 time to fit residues: 81.7286 Evaluate side-chains 205 residues out of total 3159 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 205 time to evaluate : 1.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 8.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 0.6980 chunk 244 optimal weight: 0.9980 chunk 183 optimal weight: 6.9990 chunk 298 optimal weight: 0.4980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 39 GLN D 77 ASN F 39 GLN F 82 GLN F 84 ASN B 609 GLN B 897 GLN B 953 GLN ** C 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 391 ASN ** C 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 419 ASN C 673 GLN C1138 GLN A 336 HIS A 340 ASN A 411 GLN A 609 GLN A1006 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.111592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.069125 restraints weight = 74272.454| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 3.60 r_work: 0.2980 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.1316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 29501 Z= 0.132 Angle : 0.610 10.172 40191 Z= 0.315 Chirality : 0.044 0.270 4540 Planarity : 0.005 0.063 5156 Dihedral : 5.696 59.933 4464 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.21 % Favored : 94.57 % Rotamer: Outliers : 0.60 % Allowed : 5.57 % Favored : 93.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.37 (0.13), residues: 3609 helix: 1.35 (0.21), residues: 658 sheet: -0.01 (0.18), residues: 799 loop : -2.13 (0.12), residues: 2152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 38 TYR 0.028 0.001 TYR B 38 PHE 0.022 0.001 PHE A 588 TRP 0.026 0.002 TRP F 36 HIS 0.009 0.001 HIS F 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.13 (29440) covalent geometry : angle 0.60295 / 0.31 (40043) SS BOND : bond 0.00209 / 0.13 ( 35) SS BOND : angle 0.96953 / 0.63 ( 70) hydrogen bonds : bond 0.04719 / 3.16 ( 956) hydrogen bonds : angle 5.49551 / 3.77 ( 2664) link_BETA1-4 : bond 0.00286 / 0.20 ( 11) link_BETA1-4 : angle 1.48892 / 0.87 ( 33) link_NAG-ASN : bond 0.00295 / 0.14 ( 15) link_NAG-ASN : angle 2.37665 / 1.67 ( 45) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7218 Ramachandran restraints generated. 3609 Oldfield, 0 Emsley, 3609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7218 Ramachandran restraints generated. 3609 Oldfield, 0 Emsley, 3609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 3159 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 231 time to evaluate : 1.051 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: D 38 ARG cc_start: 0.8882 (ptt-90) cc_final: 0.8648 (ttm110) REVERT: D 78 THR cc_start: 0.6663 (t) cc_final: 0.6420 (m) REVERT: E 110 TYR cc_start: 0.8239 (t80) cc_final: 0.7506 (t80) REVERT: B 87 ASP cc_start: 0.8275 (m-30) cc_final: 0.7986 (m-30) REVERT: B 198 TYR cc_start: 0.8880 (m-80) cc_final: 0.8677 (m-80) REVERT: B 1140 GLU cc_start: 0.8061 (mt-10) cc_final: 0.7662 (pp20) REVERT: C 158 TYR cc_start: 0.4421 (m-10) cc_final: 0.3979 (p90) REVERT: C 175 MET cc_start: 0.5732 (mmp) cc_final: 0.5359 (ptt) REVERT: C 418 TYR cc_start: 0.7182 (m-80) cc_final: 0.6726 (m-80) REVERT: C 979 ARG cc_start: 0.8544 (ptm160) cc_final: 0.8227 (ptm-80) REVERT: A 402 ASN cc_start: 0.8236 (t0) cc_final: 0.7834 (m110) REVERT: A 981 ASP cc_start: 0.8503 (m-30) cc_final: 0.7991 (m-30) REVERT: A 990 ASP cc_start: 0.8202 (p0) cc_final: 0.7690 (t0) outliers start: 19 outliers final: 10 residues processed: 244 average time/residue: 0.1751 time to fit residues: 70.9638 Evaluate side-chains 206 residues out of total 3159 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 196 time to evaluate : 1.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 94 TYR Chi-restraints excluded: chain D residue 125 VAL Chi-restraints excluded: chain F residue 84 ASN Chi-restraints excluded: chain B residue 425 ASP Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain C residue 126 PHE Chi-restraints excluded: chain C residue 230 ILE Chi-restraints excluded: chain C residue 386 ASP Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 506 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 196 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 chunk 116 optimal weight: 0.8980 chunk 299 optimal weight: 0.9980 chunk 15 optimal weight: 7.9990 chunk 206 optimal weight: 0.9990 chunk 50 optimal weight: 8.9990 chunk 226 optimal weight: 0.6980 chunk 94 optimal weight: 3.9990 chunk 174 optimal weight: 0.8980 chunk 301 optimal weight: 30.0000 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 13 GLN F 84 ASN B 144 HIS B 367 ASN B 931 GLN ** C 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 609 GLN ** C 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 336 HIS A 411 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.110705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.067978 restraints weight = 74190.073| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 3.59 r_work: 0.2950 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.1679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 29501 Z= 0.128 Angle : 0.571 8.575 40191 Z= 0.292 Chirality : 0.044 0.252 4540 Planarity : 0.004 0.061 5156 Dihedral : 5.364 59.884 4464 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.25 % Allowed : 4.90 % Favored : 94.85 % Rotamer: Outliers : 1.08 % Allowed : 6.77 % Favored : 92.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.05 (0.14), residues: 3609 helix: 1.95 (0.21), residues: 653 sheet: 0.15 (0.18), residues: 808 loop : -2.03 (0.12), residues: 2148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 72 TYR 0.028 0.001 TYR B 38 PHE 0.021 0.001 PHE A 339 TRP 0.023 0.001 TRP A 449 HIS 0.008 0.001 HIS F 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.13 (29440) covalent geometry : angle 0.56491 / 0.29 (40043) SS BOND : bond 0.00201 / 0.12 ( 35) SS BOND : angle 0.90508 / 0.59 ( 70) hydrogen bonds : bond 0.04291 / 2.84 ( 956) hydrogen bonds : angle 5.07845 / 3.48 ( 2664) link_BETA1-4 : bond 0.00199 / 0.14 ( 11) link_BETA1-4 : angle 1.39948 / 0.83 ( 33) link_NAG-ASN : bond 0.00191 / 0.09 ( 15) link_NAG-ASN : angle 2.22394 / 1.56 ( 45) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7218 Ramachandran restraints generated. 3609 Oldfield, 0 Emsley, 3609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7218 Ramachandran restraints generated. 3609 Oldfield, 0 Emsley, 3609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 3159 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 208 time to evaluate : 1.238 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 78 THR cc_start: 0.6791 (t) cc_final: 0.6557 (m) REVERT: D 82 GLN cc_start: 0.8088 (tm-30) cc_final: 0.7839 (mp10) REVERT: E 68 PHE cc_start: 0.7232 (m-10) cc_final: 0.6892 (m-80) REVERT: E 82 GLN cc_start: 0.8673 (tp40) cc_final: 0.8402 (tp40) REVERT: E 110 TYR cc_start: 0.8321 (t80) cc_final: 0.7860 (t80) REVERT: E 114 ASP cc_start: 0.8803 (p0) cc_final: 0.8594 (p0) REVERT: B 87 ASP cc_start: 0.8330 (m-30) cc_final: 0.8100 (m-30) REVERT: B 1140 GLU cc_start: 0.8098 (mt-10) cc_final: 0.7841 (mm-30) REVERT: C 175 MET cc_start: 0.5782 (mmp) cc_final: 0.5295 (ptt) REVERT: C 418 TYR cc_start: 0.7132 (m-80) cc_final: 0.6707 (m-80) REVERT: C 979 ARG cc_start: 0.8559 (ptm160) cc_final: 0.8252 (ptm-80) REVERT: A 402 ASN cc_start: 0.8244 (t0) cc_final: 0.7831 (m110) REVERT: A 449 TRP cc_start: 0.8624 (m100) cc_final: 0.8185 (m100) REVERT: A 693 MET cc_start: 0.8921 (mmm) cc_final: 0.8592 (mtt) REVERT: A 981 ASP cc_start: 0.8468 (m-30) cc_final: 0.8201 (m-30) REVERT: A 990 ASP cc_start: 0.8203 (p0) cc_final: 0.7750 (t0) outliers start: 34 outliers final: 24 residues processed: 230 average time/residue: 0.1720 time to fit residues: 66.7747 Evaluate side-chains 213 residues out of total 3159 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 189 time to evaluate : 1.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 94 TYR Chi-restraints excluded: chain D residue 125 VAL Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain B residue 126 PHE Chi-restraints excluded: chain B residue 425 ASP Chi-restraints excluded: chain B residue 626 THR Chi-restraints excluded: chain B residue 936 SER Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1090 VAL Chi-restraints excluded: chain C residue 126 PHE Chi-restraints excluded: chain C residue 230 ILE Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 346 SER Chi-restraints excluded: chain C residue 386 ASP Chi-restraints excluded: chain C residue 433 TRP Chi-restraints excluded: chain C residue 566 VAL Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 411 GLN Chi-restraints excluded: chain A residue 506 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 92 optimal weight: 2.9990 chunk 246 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 chunk 180 optimal weight: 5.9990 chunk 197 optimal weight: 5.9990 chunk 238 optimal weight: 1.9990 chunk 159 optimal weight: 5.9990 chunk 301 optimal weight: 0.8980 chunk 250 optimal weight: 2.9990 chunk 332 optimal weight: 2.9990 chunk 33 optimal weight: 20.0000 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 84 ASN ** B 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 336 HIS ** C 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 419 ASN C 536 ASN ** C 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 751 GLN A 336 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.106034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.062390 restraints weight = 73841.561| |-----------------------------------------------------------------------------| r_work (start): 0.2966 rms_B_bonded: 3.61 r_work: 0.2827 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.2503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 29501 Z= 0.260 Angle : 0.663 11.185 40191 Z= 0.339 Chirality : 0.047 0.273 4540 Planarity : 0.005 0.058 5156 Dihedral : 5.576 59.863 4464 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.26 % Favored : 93.52 % Rotamer: Outliers : 1.49 % Allowed : 9.28 % Favored : 89.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.07 (0.14), residues: 3609 helix: 1.91 (0.21), residues: 658 sheet: 0.02 (0.18), residues: 828 loop : -2.00 (0.12), residues: 2123 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C1087 TYR 0.029 0.002 TYR B 38 PHE 0.030 0.002 PHE B 902 TRP 0.016 0.002 TRP A1098 HIS 0.006 0.001 HIS F 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00634 / 0.26 (29440) covalent geometry : angle 0.65268 / 0.34 (40043) SS BOND : bond 0.00332 / 0.20 ( 35) SS BOND : angle 1.68355 / 1.06 ( 70) hydrogen bonds : bond 0.05421 / 3.55 ( 956) hydrogen bonds : angle 5.04867 / 3.48 ( 2664) link_BETA1-4 : bond 0.00256 / 0.18 ( 11) link_BETA1-4 : angle 1.52598 / 0.94 ( 33) link_NAG-ASN : bond 0.00431 / 0.23 ( 15) link_NAG-ASN : angle 2.71672 / 1.88 ( 45) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7218 Ramachandran restraints generated. 3609 Oldfield, 0 Emsley, 3609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7218 Ramachandran restraints generated. 3609 Oldfield, 0 Emsley, 3609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 3159 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 203 time to evaluate : 1.118 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 57 THR cc_start: 0.7620 (OUTLIER) cc_final: 0.6981 (t) REVERT: D 60 TYR cc_start: 0.6539 (m-80) cc_final: 0.6199 (m-10) REVERT: E 68 PHE cc_start: 0.7732 (m-10) cc_final: 0.7459 (m-80) REVERT: E 110 TYR cc_start: 0.8395 (t80) cc_final: 0.8007 (t80) REVERT: E 114 ASP cc_start: 0.8873 (p0) cc_final: 0.8584 (p0) REVERT: C 175 MET cc_start: 0.5960 (mmp) cc_final: 0.5196 (ptt) REVERT: C 418 TYR cc_start: 0.7020 (m-80) cc_final: 0.6569 (m-80) REVERT: C 565 ILE cc_start: 0.9001 (OUTLIER) cc_final: 0.8760 (mp) REVERT: C 736 MET cc_start: 0.9363 (OUTLIER) cc_final: 0.9088 (ttt) REVERT: C 979 ARG cc_start: 0.8606 (ptm160) cc_final: 0.8277 (ptm-80) REVERT: A 167 GLU cc_start: 0.8102 (tp30) cc_final: 0.7609 (mp0) REVERT: A 402 ASN cc_start: 0.8347 (t0) cc_final: 0.7968 (m110) REVERT: A 981 ASP cc_start: 0.8554 (m-30) cc_final: 0.8309 (m-30) outliers start: 47 outliers final: 23 residues processed: 239 average time/residue: 0.1816 time to fit residues: 71.4549 Evaluate side-chains 211 residues out of total 3159 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 185 time to evaluate : 1.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 57 THR Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 125 VAL Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain F residue 84 ASN Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 425 ASP Chi-restraints excluded: chain B residue 584 THR Chi-restraints excluded: chain B residue 626 THR Chi-restraints excluded: chain B residue 936 SER Chi-restraints excluded: chain B residue 953 GLN Chi-restraints excluded: chain B residue 1090 VAL Chi-restraints excluded: chain C residue 118 ILE Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 346 SER Chi-restraints excluded: chain C residue 386 ASP Chi-restraints excluded: chain C residue 509 LEU Chi-restraints excluded: chain C residue 565 ILE Chi-restraints excluded: chain C residue 566 VAL Chi-restraints excluded: chain C residue 645 CYS Chi-restraints excluded: chain C residue 736 MET Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 506 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 39 optimal weight: 3.9990 chunk 310 optimal weight: 0.8980 chunk 81 optimal weight: 1.9990 chunk 299 optimal weight: 9.9990 chunk 115 optimal weight: 0.8980 chunk 331 optimal weight: 0.8980 chunk 163 optimal weight: 2.9990 chunk 357 optimal weight: 0.9990 chunk 314 optimal weight: 0.4980 chunk 266 optimal weight: 4.9990 chunk 292 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 419 ASN C 673 GLN C 751 GLN A 336 HIS ** A 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.107660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.064301 restraints weight = 73849.744| |-----------------------------------------------------------------------------| r_work (start): 0.3007 rms_B_bonded: 3.61 r_work: 0.2869 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.2616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 29501 Z= 0.122 Angle : 0.574 13.362 40191 Z= 0.290 Chirality : 0.043 0.271 4540 Planarity : 0.004 0.057 5156 Dihedral : 5.329 59.716 4464 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.25 % Allowed : 4.99 % Favored : 94.76 % Rotamer: Outliers : 1.39 % Allowed : 10.51 % Favored : 88.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.89 (0.14), residues: 3609 helix: 2.27 (0.21), residues: 654 sheet: 0.18 (0.18), residues: 817 loop : -1.97 (0.12), residues: 2138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 38 TYR 0.029 0.001 TYR E 59 PHE 0.021 0.001 PHE C 511 TRP 0.029 0.001 TRP A 449 HIS 0.006 0.001 HIS F 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.12 (29440) covalent geometry : angle 0.56685 / 0.29 (40043) SS BOND : bond 0.00215 / 0.12 ( 35) SS BOND : angle 1.22090 / 0.74 ( 70) hydrogen bonds : bond 0.04365 / 2.86 ( 956) hydrogen bonds : angle 4.76678 / 3.28 ( 2664) link_BETA1-4 : bond 0.00237 / 0.15 ( 11) link_BETA1-4 : angle 1.34925 / 0.80 ( 33) link_NAG-ASN : bond 0.00235 / 0.11 ( 15) link_NAG-ASN : angle 2.24035 / 1.57 ( 45) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7218 Ramachandran restraints generated. 3609 Oldfield, 0 Emsley, 3609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7218 Ramachandran restraints generated. 3609 Oldfield, 0 Emsley, 3609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 3159 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 197 time to evaluate : 0.893 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 60 TYR cc_start: 0.6468 (m-80) cc_final: 0.6253 (m-10) REVERT: D 80 TYR cc_start: 0.6690 (m-10) cc_final: 0.6033 (m-10) REVERT: E 110 TYR cc_start: 0.8409 (t80) cc_final: 0.8033 (t80) REVERT: E 114 ASP cc_start: 0.8886 (p0) cc_final: 0.8498 (p0) REVERT: F 36 TRP cc_start: 0.4067 (t-100) cc_final: 0.3324 (t-100) REVERT: F 46 GLU cc_start: 0.8094 (tp30) cc_final: 0.7780 (tm-30) REVERT: B 415 ILE cc_start: 0.9074 (OUTLIER) cc_final: 0.8870 (mp) REVERT: C 158 TYR cc_start: 0.4268 (m-10) cc_final: 0.3726 (p90) REVERT: C 175 MET cc_start: 0.5951 (mmp) cc_final: 0.5420 (ptt) REVERT: C 339 PHE cc_start: 0.8550 (m-10) cc_final: 0.8281 (t80) REVERT: C 418 TYR cc_start: 0.6976 (m-80) cc_final: 0.6517 (m-80) REVERT: C 770 GLN cc_start: 0.9140 (OUTLIER) cc_final: 0.8759 (mp10) REVERT: C 979 ARG cc_start: 0.8623 (ptm160) cc_final: 0.8296 (ptm-80) REVERT: A 167 GLU cc_start: 0.8074 (tp30) cc_final: 0.7582 (mp0) REVERT: A 383 LYS cc_start: 0.9547 (mmmt) cc_final: 0.8981 (tptt) REVERT: A 402 ASN cc_start: 0.8373 (t0) cc_final: 0.7997 (m110) REVERT: A 625 LEU cc_start: 0.5826 (mt) cc_final: 0.5588 (mt) REVERT: A 981 ASP cc_start: 0.8491 (m-30) cc_final: 0.8244 (m-30) outliers start: 44 outliers final: 26 residues processed: 231 average time/residue: 0.1690 time to fit residues: 65.4458 Evaluate side-chains 214 residues out of total 3159 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 186 time to evaluate : 1.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain B residue 126 PHE Chi-restraints excluded: chain B residue 415 ILE Chi-restraints excluded: chain B residue 425 ASP Chi-restraints excluded: chain B residue 565 ILE Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 626 THR Chi-restraints excluded: chain B residue 936 SER Chi-restraints excluded: chain B residue 1090 VAL Chi-restraints excluded: chain C residue 118 ILE Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 346 SER Chi-restraints excluded: chain C residue 386 ASP Chi-restraints excluded: chain C residue 433 TRP Chi-restraints excluded: chain C residue 509 LEU Chi-restraints excluded: chain C residue 566 VAL Chi-restraints excluded: chain C residue 645 CYS Chi-restraints excluded: chain C residue 736 MET Chi-restraints excluded: chain C residue 770 GLN Chi-restraints excluded: chain C residue 782 LYS Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 577 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 187 optimal weight: 4.9990 chunk 245 optimal weight: 0.6980 chunk 252 optimal weight: 9.9990 chunk 43 optimal weight: 1.9990 chunk 130 optimal weight: 0.5980 chunk 181 optimal weight: 0.9980 chunk 163 optimal weight: 0.9980 chunk 59 optimal weight: 0.8980 chunk 128 optimal weight: 0.9990 chunk 121 optimal weight: 0.8980 chunk 222 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 747 ASN B 953 GLN C 114 GLN ** C 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 336 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.107842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.064702 restraints weight = 73913.144| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 3.59 r_work: 0.2877 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.2733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 29501 Z= 0.116 Angle : 0.559 14.539 40191 Z= 0.280 Chirality : 0.043 0.261 4540 Planarity : 0.004 0.055 5156 Dihedral : 5.118 56.084 4464 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.35 % Favored : 94.46 % Rotamer: Outliers : 1.46 % Allowed : 10.83 % Favored : 87.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.79 (0.14), residues: 3609 helix: 2.36 (0.21), residues: 658 sheet: 0.23 (0.18), residues: 805 loop : -1.90 (0.12), residues: 2146 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 38 TYR 0.019 0.001 TYR C 158 PHE 0.019 0.001 PHE C 371 TRP 0.021 0.001 TRP A 449 HIS 0.006 0.001 HIS F 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 (29440) covalent geometry : angle 0.55183 / 0.28 (40043) SS BOND : bond 0.00308 / 0.13 ( 35) SS BOND : angle 1.02567 / 0.64 ( 70) hydrogen bonds : bond 0.04049 / 2.65 ( 956) hydrogen bonds : angle 4.61778 / 3.18 ( 2664) link_BETA1-4 : bond 0.00264 / 0.14 ( 11) link_BETA1-4 : angle 1.35326 / 0.81 ( 33) link_NAG-ASN : bond 0.00227 / 0.10 ( 15) link_NAG-ASN : angle 2.18966 / 1.51 ( 45) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7218 Ramachandran restraints generated. 3609 Oldfield, 0 Emsley, 3609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7218 Ramachandran restraints generated. 3609 Oldfield, 0 Emsley, 3609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 3159 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 207 time to evaluate : 1.120 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 94 TYR cc_start: 0.8078 (m-80) cc_final: 0.7663 (m-10) REVERT: E 68 PHE cc_start: 0.7185 (m-80) cc_final: 0.6683 (m-80) REVERT: E 110 TYR cc_start: 0.8431 (t80) cc_final: 0.7998 (t80) REVERT: E 114 ASP cc_start: 0.8913 (p0) cc_final: 0.8651 (p0) REVERT: F 36 TRP cc_start: 0.4215 (t-100) cc_final: 0.3967 (t-100) REVERT: F 46 GLU cc_start: 0.8092 (tp30) cc_final: 0.7800 (tm-30) REVERT: B 198 TYR cc_start: 0.8893 (m-80) cc_final: 0.7868 (t80) REVERT: B 415 ILE cc_start: 0.9075 (OUTLIER) cc_final: 0.8872 (mp) REVERT: C 158 TYR cc_start: 0.4392 (m-10) cc_final: 0.3989 (p90) REVERT: C 175 MET cc_start: 0.5957 (mmp) cc_final: 0.5650 (ptt) REVERT: C 339 PHE cc_start: 0.8548 (m-10) cc_final: 0.8268 (t80) REVERT: C 418 TYR cc_start: 0.6986 (m-80) cc_final: 0.6531 (m-80) REVERT: C 565 ILE cc_start: 0.9048 (OUTLIER) cc_final: 0.8789 (mt) REVERT: C 851 PHE cc_start: 0.7322 (m-10) cc_final: 0.7119 (m-10) REVERT: C 979 ARG cc_start: 0.8616 (ptm160) cc_final: 0.8304 (ptm-80) REVERT: A 167 GLU cc_start: 0.8012 (tp30) cc_final: 0.7552 (mp0) REVERT: A 383 LYS cc_start: 0.9527 (mmmt) cc_final: 0.8953 (tptt) REVERT: A 402 ASN cc_start: 0.8316 (t0) cc_final: 0.7961 (m-40) REVERT: A 851 PHE cc_start: 0.8132 (m-10) cc_final: 0.7896 (m-10) REVERT: A 981 ASP cc_start: 0.8469 (m-30) cc_final: 0.8221 (m-30) outliers start: 46 outliers final: 31 residues processed: 243 average time/residue: 0.1722 time to fit residues: 70.4766 Evaluate side-chains 222 residues out of total 3159 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 189 time to evaluate : 1.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain F residue 84 ASN Chi-restraints excluded: chain B residue 126 PHE Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 415 ILE Chi-restraints excluded: chain B residue 425 ASP Chi-restraints excluded: chain B residue 565 ILE Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 626 THR Chi-restraints excluded: chain B residue 759 LEU Chi-restraints excluded: chain B residue 936 SER Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain C residue 118 ILE Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 213 PHE Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 346 SER Chi-restraints excluded: chain C residue 433 TRP Chi-restraints excluded: chain C residue 509 LEU Chi-restraints excluded: chain C residue 565 ILE Chi-restraints excluded: chain C residue 566 VAL Chi-restraints excluded: chain C residue 736 MET Chi-restraints excluded: chain C residue 782 LYS Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 417 ASP Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 577 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 29 optimal weight: 6.9990 chunk 106 optimal weight: 0.8980 chunk 143 optimal weight: 0.0370 chunk 224 optimal weight: 0.1980 chunk 130 optimal weight: 0.7980 chunk 253 optimal weight: 1.9990 chunk 114 optimal weight: 1.9990 chunk 339 optimal weight: 7.9990 chunk 43 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 351 optimal weight: 3.9990 overall best weight: 0.7860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 336 HIS A 340 ASN ** A 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.107745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.064763 restraints weight = 73889.259| |-----------------------------------------------------------------------------| r_work (start): 0.3020 rms_B_bonded: 3.62 r_work: 0.2883 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.2889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 29501 Z= 0.117 Angle : 0.558 15.185 40191 Z= 0.279 Chirality : 0.043 0.251 4540 Planarity : 0.004 0.062 5156 Dihedral : 4.983 55.565 4464 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.10 % Favored : 94.74 % Rotamer: Outliers : 1.33 % Allowed : 11.93 % Favored : 86.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3609 helix: 2.44 (0.21), residues: 661 sheet: 0.27 (0.18), residues: 815 loop : -1.84 (0.12), residues: 2133 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 101 TYR 0.017 0.001 TYR C 158 PHE 0.020 0.001 PHE A 339 TRP 0.017 0.001 TRP A 449 HIS 0.006 0.001 HIS F 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.12 (29440) covalent geometry : angle 0.55176 / 0.28 (40043) SS BOND : bond 0.00228 / 0.12 ( 35) SS BOND : angle 1.02805 / 0.64 ( 70) hydrogen bonds : bond 0.03969 / 2.61 ( 956) hydrogen bonds : angle 4.53826 / 3.13 ( 2664) link_BETA1-4 : bond 0.00242 / 0.15 ( 11) link_BETA1-4 : angle 1.32570 / 0.80 ( 33) link_NAG-ASN : bond 0.00221 / 0.10 ( 15) link_NAG-ASN : angle 2.17355 / 1.49 ( 45) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7218 Ramachandran restraints generated. 3609 Oldfield, 0 Emsley, 3609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7218 Ramachandran restraints generated. 3609 Oldfield, 0 Emsley, 3609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 3159 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 201 time to evaluate : 1.254 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 80 TYR cc_start: 0.6615 (m-10) cc_final: 0.5882 (m-10) REVERT: E 110 TYR cc_start: 0.8493 (t80) cc_final: 0.8129 (t80) REVERT: E 114 ASP cc_start: 0.8946 (p0) cc_final: 0.8697 (p0) REVERT: F 83 MET cc_start: 0.6731 (tpp) cc_final: 0.6336 (tmm) REVERT: B 198 TYR cc_start: 0.8859 (m-80) cc_final: 0.7821 (t80) REVERT: B 415 ILE cc_start: 0.9080 (OUTLIER) cc_final: 0.8873 (mp) REVERT: C 293 LEU cc_start: 0.8111 (OUTLIER) cc_final: 0.7886 (tp) REVERT: C 339 PHE cc_start: 0.8587 (m-10) cc_final: 0.8301 (t80) REVERT: C 565 ILE cc_start: 0.9035 (OUTLIER) cc_final: 0.8780 (mt) REVERT: C 770 GLN cc_start: 0.9139 (OUTLIER) cc_final: 0.8744 (mp10) REVERT: C 979 ARG cc_start: 0.8620 (ptm160) cc_final: 0.8295 (ptm-80) REVERT: A 167 GLU cc_start: 0.8007 (tp30) cc_final: 0.7577 (mp0) REVERT: A 402 ASN cc_start: 0.8328 (t0) cc_final: 0.7983 (m-40) REVERT: A 426 PHE cc_start: 0.8756 (t80) cc_final: 0.8311 (t80) REVERT: A 851 PHE cc_start: 0.8167 (m-10) cc_final: 0.7926 (m-10) REVERT: A 981 ASP cc_start: 0.8461 (m-30) cc_final: 0.8205 (m-30) outliers start: 42 outliers final: 28 residues processed: 234 average time/residue: 0.1709 time to fit residues: 67.4981 Evaluate side-chains 224 residues out of total 3159 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 192 time to evaluate : 1.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 104 CYS Chi-restraints excluded: chain F residue 29 LEU Chi-restraints excluded: chain B residue 126 PHE Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 415 ILE Chi-restraints excluded: chain B residue 425 ASP Chi-restraints excluded: chain B residue 565 ILE Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 626 THR Chi-restraints excluded: chain B residue 759 LEU Chi-restraints excluded: chain B residue 936 SER Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 213 PHE Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 346 SER Chi-restraints excluded: chain C residue 433 TRP Chi-restraints excluded: chain C residue 509 LEU Chi-restraints excluded: chain C residue 565 ILE Chi-restraints excluded: chain C residue 736 MET Chi-restraints excluded: chain C residue 770 GLN Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 577 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 68 optimal weight: 0.3980 chunk 150 optimal weight: 6.9990 chunk 23 optimal weight: 0.0070 chunk 300 optimal weight: 8.9990 chunk 187 optimal weight: 0.0170 chunk 148 optimal weight: 0.8980 chunk 299 optimal weight: 6.9990 chunk 208 optimal weight: 4.9990 chunk 31 optimal weight: 4.9990 chunk 66 optimal weight: 0.1980 chunk 282 optimal weight: 0.9980 overall best weight: 0.3036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN ** B 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 336 HIS A 576 GLN A 758 GLN A 953 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.108717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.065891 restraints weight = 74238.964| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 3.62 r_work: 0.2911 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.2958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 29501 Z= 0.096 Angle : 0.549 14.412 40191 Z= 0.274 Chirality : 0.043 0.278 4540 Planarity : 0.004 0.059 5156 Dihedral : 4.774 54.391 4464 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.15 % Favored : 94.68 % Rotamer: Outliers : 1.36 % Allowed : 12.28 % Favored : 86.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.61 (0.14), residues: 3609 helix: 2.54 (0.21), residues: 663 sheet: 0.32 (0.18), residues: 815 loop : -1.80 (0.12), residues: 2131 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 38 TYR 0.027 0.001 TYR C 158 PHE 0.023 0.001 PHE B 344 TRP 0.018 0.001 TRP A 433 HIS 0.006 0.001 HIS D 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.10 (29440) covalent geometry : angle 0.54268 / 0.27 (40043) SS BOND : bond 0.00193 / 0.10 ( 35) SS BOND : angle 0.93020 / 0.58 ( 70) hydrogen bonds : bond 0.03563 / 2.34 ( 956) hydrogen bonds : angle 4.43385 / 3.05 ( 2664) link_BETA1-4 : bond 0.00365 / 0.23 ( 11) link_BETA1-4 : angle 1.30244 / 0.77 ( 33) link_NAG-ASN : bond 0.00270 / 0.13 ( 15) link_NAG-ASN : angle 2.03152 / 1.38 ( 45) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7218 Ramachandran restraints generated. 3609 Oldfield, 0 Emsley, 3609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7218 Ramachandran restraints generated. 3609 Oldfield, 0 Emsley, 3609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 3159 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 205 time to evaluate : 1.124 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 82 GLN cc_start: 0.8153 (tm-30) cc_final: 0.7945 (mp10) REVERT: E 68 PHE cc_start: 0.7287 (m-80) cc_final: 0.6759 (m-80) REVERT: E 110 TYR cc_start: 0.8533 (t80) cc_final: 0.8166 (t80) REVERT: E 114 ASP cc_start: 0.8991 (p0) cc_final: 0.8776 (p0) REVERT: B 198 TYR cc_start: 0.8818 (m-80) cc_final: 0.7813 (t80) REVERT: B 277 ASN cc_start: 0.8378 (t0) cc_final: 0.8170 (t0) REVERT: C 158 TYR cc_start: 0.4221 (m-10) cc_final: 0.3756 (p90) REVERT: C 175 MET cc_start: 0.6427 (OUTLIER) cc_final: 0.6073 (mmm) REVERT: C 339 PHE cc_start: 0.8587 (m-10) cc_final: 0.8269 (t80) REVERT: C 565 ILE cc_start: 0.9061 (OUTLIER) cc_final: 0.8795 (mt) REVERT: C 770 GLN cc_start: 0.9078 (OUTLIER) cc_final: 0.8710 (mp10) REVERT: C 979 ARG cc_start: 0.8627 (ptm160) cc_final: 0.8312 (ptm-80) REVERT: A 167 GLU cc_start: 0.7970 (tp30) cc_final: 0.7527 (mp0) REVERT: A 402 ASN cc_start: 0.8344 (t0) cc_final: 0.8009 (m-40) REVERT: A 426 PHE cc_start: 0.8815 (t80) cc_final: 0.8399 (t80) REVERT: A 851 PHE cc_start: 0.8181 (m-10) cc_final: 0.7924 (m-10) REVERT: A 981 ASP cc_start: 0.8406 (m-30) cc_final: 0.8139 (m-30) outliers start: 43 outliers final: 30 residues processed: 235 average time/residue: 0.1689 time to fit residues: 66.6865 Evaluate side-chains 224 residues out of total 3159 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 191 time to evaluate : 1.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain E residue 104 CYS Chi-restraints excluded: chain B residue 126 PHE Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 425 ASP Chi-restraints excluded: chain B residue 565 ILE Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 626 THR Chi-restraints excluded: chain B residue 759 LEU Chi-restraints excluded: chain B residue 936 SER Chi-restraints excluded: chain C residue 175 MET Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 213 PHE Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 346 SER Chi-restraints excluded: chain C residue 433 TRP Chi-restraints excluded: chain C residue 511 PHE Chi-restraints excluded: chain C residue 565 ILE Chi-restraints excluded: chain C residue 566 VAL Chi-restraints excluded: chain C residue 736 MET Chi-restraints excluded: chain C residue 770 GLN Chi-restraints excluded: chain C residue 776 GLU Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 577 THR Chi-restraints excluded: chain A residue 581 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 72 optimal weight: 0.9990 chunk 16 optimal weight: 8.9990 chunk 312 optimal weight: 0.9980 chunk 335 optimal weight: 0.9990 chunk 294 optimal weight: 10.0000 chunk 84 optimal weight: 2.9990 chunk 183 optimal weight: 5.9990 chunk 21 optimal weight: 7.9990 chunk 33 optimal weight: 10.0000 chunk 332 optimal weight: 2.9990 chunk 164 optimal weight: 4.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 84 ASN ** B 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 336 HIS ** A 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 758 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.105513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.062274 restraints weight = 74003.423| |-----------------------------------------------------------------------------| r_work (start): 0.2962 rms_B_bonded: 3.60 r_work: 0.2822 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8660 moved from start: 0.3220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 29501 Z= 0.200 Angle : 0.615 14.249 40191 Z= 0.308 Chirality : 0.045 0.280 4540 Planarity : 0.004 0.055 5156 Dihedral : 5.036 57.637 4464 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.18 % Favored : 93.65 % Rotamer: Outliers : 1.27 % Allowed : 12.66 % Favored : 86.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.68 (0.14), residues: 3609 helix: 2.42 (0.21), residues: 662 sheet: 0.25 (0.18), residues: 842 loop : -1.83 (0.13), residues: 2105 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 505 TYR 0.026 0.001 TYR C 158 PHE 0.022 0.002 PHE A 339 TRP 0.013 0.002 TRP C 433 HIS 0.006 0.001 HIS F 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00481 / 0.20 (29440) covalent geometry : angle 0.60661 / 0.31 (40043) SS BOND : bond 0.00311 / 0.18 ( 35) SS BOND : angle 1.28026 / 0.79 ( 70) hydrogen bonds : bond 0.04735 / 3.10 ( 956) hydrogen bonds : angle 4.61012 / 3.17 ( 2664) link_BETA1-4 : bond 0.00156 / 0.12 ( 11) link_BETA1-4 : angle 1.38559 / 0.86 ( 33) link_NAG-ASN : bond 0.00340 / 0.17 ( 15) link_NAG-ASN : angle 2.56019 / 1.74 ( 45) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7218 Ramachandran restraints generated. 3609 Oldfield, 0 Emsley, 3609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7218 Ramachandran restraints generated. 3609 Oldfield, 0 Emsley, 3609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 3159 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 191 time to evaluate : 1.156 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 68 PHE cc_start: 0.7416 (m-80) cc_final: 0.6941 (m-80) REVERT: E 110 TYR cc_start: 0.8564 (t80) cc_final: 0.8204 (t80) REVERT: E 114 ASP cc_start: 0.8955 (p0) cc_final: 0.8682 (p0) REVERT: F 83 MET cc_start: 0.5919 (tpp) cc_final: 0.5337 (tmm) REVERT: B 198 TYR cc_start: 0.8882 (m-80) cc_final: 0.7800 (t80) REVERT: C 158 TYR cc_start: 0.4368 (m-10) cc_final: 0.3984 (p90) REVERT: C 293 LEU cc_start: 0.8313 (OUTLIER) cc_final: 0.8055 (tp) REVERT: C 339 PHE cc_start: 0.8651 (m-10) cc_final: 0.8324 (t80) REVERT: C 736 MET cc_start: 0.9376 (OUTLIER) cc_final: 0.9113 (ttt) REVERT: C 770 GLN cc_start: 0.9236 (OUTLIER) cc_final: 0.8803 (mp10) REVERT: C 979 ARG cc_start: 0.8621 (ptm160) cc_final: 0.8288 (ptm-80) REVERT: A 167 GLU cc_start: 0.7957 (tp30) cc_final: 0.7653 (mp0) REVERT: A 402 ASN cc_start: 0.8313 (t0) cc_final: 0.7962 (m110) REVERT: A 426 PHE cc_start: 0.8843 (t80) cc_final: 0.8455 (t80) REVERT: A 981 ASP cc_start: 0.8505 (m-30) cc_final: 0.8241 (m-30) outliers start: 40 outliers final: 33 residues processed: 221 average time/residue: 0.1721 time to fit residues: 64.0811 Evaluate side-chains 224 residues out of total 3159 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 188 time to evaluate : 1.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 39 GLN Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain E residue 104 CYS Chi-restraints excluded: chain F residue 29 LEU Chi-restraints excluded: chain F residue 84 ASN Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 425 ASP Chi-restraints excluded: chain B residue 565 ILE Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 584 THR Chi-restraints excluded: chain B residue 626 THR Chi-restraints excluded: chain B residue 759 LEU Chi-restraints excluded: chain B residue 936 SER Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 213 PHE Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 346 SER Chi-restraints excluded: chain C residue 433 TRP Chi-restraints excluded: chain C residue 511 PHE Chi-restraints excluded: chain C residue 566 VAL Chi-restraints excluded: chain C residue 736 MET Chi-restraints excluded: chain C residue 770 GLN Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 417 ASP Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 577 THR Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 701 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 10 optimal weight: 5.9990 chunk 136 optimal weight: 2.9990 chunk 3 optimal weight: 10.0000 chunk 329 optimal weight: 0.6980 chunk 145 optimal weight: 3.9990 chunk 200 optimal weight: 0.8980 chunk 199 optimal weight: 0.8980 chunk 180 optimal weight: 4.9990 chunk 356 optimal weight: 0.9980 chunk 59 optimal weight: 0.9990 chunk 297 optimal weight: 9.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 336 HIS ** A 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.105722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.062525 restraints weight = 73610.639| |-----------------------------------------------------------------------------| r_work (start): 0.2967 rms_B_bonded: 3.59 r_work: 0.2830 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 moved from start: 0.3237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.095 29501 Z= 0.168 Angle : 0.721 59.197 40191 Z= 0.385 Chirality : 0.044 0.326 4540 Planarity : 0.004 0.053 5156 Dihedral : 5.040 57.633 4464 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.99 % Favored : 93.85 % Rotamer: Outliers : 1.23 % Allowed : 12.85 % Favored : 85.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.69 (0.14), residues: 3609 helix: 2.43 (0.21), residues: 662 sheet: 0.25 (0.18), residues: 842 loop : -1.83 (0.13), residues: 2105 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG D 38 TYR 0.024 0.001 TYR C 158 PHE 0.017 0.001 PHE A 339 TRP 0.013 0.002 TRP C 433 HIS 0.006 0.001 HIS F 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.17 (29440) covalent geometry : angle 0.71386 / 0.38 (40043) SS BOND : bond 0.00300 / 0.17 ( 35) SS BOND : angle 1.23270 / 0.76 ( 70) hydrogen bonds : bond 0.04655 / 3.05 ( 956) hydrogen bonds : angle 4.60797 / 3.17 ( 2664) link_BETA1-4 : bond 0.00169 / 0.13 ( 11) link_BETA1-4 : angle 1.40875 / 0.87 ( 33) link_NAG-ASN : bond 0.00347 / 0.18 ( 15) link_NAG-ASN : angle 2.55094 / 1.73 ( 45) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7218 Ramachandran restraints generated. 3609 Oldfield, 0 Emsley, 3609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7218 Ramachandran restraints generated. 3609 Oldfield, 0 Emsley, 3609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 3159 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 187 time to evaluate : 1.246 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 68 PHE cc_start: 0.7423 (m-80) cc_final: 0.6943 (m-80) REVERT: E 110 TYR cc_start: 0.8567 (t80) cc_final: 0.8237 (t80) REVERT: E 114 ASP cc_start: 0.8939 (p0) cc_final: 0.8670 (p0) REVERT: F 83 MET cc_start: 0.5968 (tpp) cc_final: 0.5274 (tmm) REVERT: B 198 TYR cc_start: 0.8879 (m-80) cc_final: 0.7798 (t80) REVERT: C 158 TYR cc_start: 0.4317 (m-10) cc_final: 0.3961 (p90) REVERT: C 293 LEU cc_start: 0.8311 (OUTLIER) cc_final: 0.8054 (tp) REVERT: C 339 PHE cc_start: 0.8656 (m-10) cc_final: 0.8335 (t80) REVERT: C 736 MET cc_start: 0.9372 (OUTLIER) cc_final: 0.9109 (ttt) REVERT: C 770 GLN cc_start: 0.9232 (OUTLIER) cc_final: 0.8802 (mp10) REVERT: C 979 ARG cc_start: 0.8624 (ptm160) cc_final: 0.8292 (ptm-80) REVERT: A 167 GLU cc_start: 0.7951 (tp30) cc_final: 0.7649 (mp0) REVERT: A 402 ASN cc_start: 0.8327 (t0) cc_final: 0.7979 (m110) REVERT: A 426 PHE cc_start: 0.8815 (t80) cc_final: 0.8452 (t80) REVERT: A 981 ASP cc_start: 0.8494 (m-30) cc_final: 0.8230 (m-30) outliers start: 39 outliers final: 34 residues processed: 214 average time/residue: 0.1656 time to fit residues: 59.9575 Evaluate side-chains 223 residues out of total 3159 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 186 time to evaluate : 1.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain E residue 104 CYS Chi-restraints excluded: chain F residue 29 LEU Chi-restraints excluded: chain F residue 94 TYR Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 425 ASP Chi-restraints excluded: chain B residue 565 ILE Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 626 THR Chi-restraints excluded: chain B residue 759 LEU Chi-restraints excluded: chain B residue 936 SER Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 213 PHE Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 346 SER Chi-restraints excluded: chain C residue 382 THR Chi-restraints excluded: chain C residue 433 TRP Chi-restraints excluded: chain C residue 511 PHE Chi-restraints excluded: chain C residue 566 VAL Chi-restraints excluded: chain C residue 736 MET Chi-restraints excluded: chain C residue 770 GLN Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 417 ASP Chi-restraints excluded: chain A residue 461 PHE Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 577 THR Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 701 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 229 optimal weight: 1.9990 chunk 164 optimal weight: 4.9990 chunk 334 optimal weight: 0.6980 chunk 179 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 242 optimal weight: 0.9990 chunk 352 optimal weight: 0.8980 chunk 55 optimal weight: 0.0980 chunk 349 optimal weight: 0.4980 chunk 219 optimal weight: 0.0470 chunk 36 optimal weight: 7.9990 overall best weight: 0.4478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 336 HIS ** A 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.105712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.062486 restraints weight = 74129.483| |-----------------------------------------------------------------------------| r_work (start): 0.2967 rms_B_bonded: 3.61 r_work: 0.2828 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.3234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.162 29501 Z= 0.175 Angle : 0.722 59.197 40191 Z= 0.386 Chirality : 0.044 0.326 4540 Planarity : 0.004 0.053 5156 Dihedral : 5.040 57.633 4464 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.99 % Favored : 93.85 % Rotamer: Outliers : 1.20 % Allowed : 12.88 % Favored : 85.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.69 (0.14), residues: 3609 helix: 2.43 (0.21), residues: 662 sheet: 0.25 (0.18), residues: 842 loop : -1.83 (0.13), residues: 2105 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG D 38 TYR 0.024 0.001 TYR C 158 PHE 0.017 0.001 PHE A 339 TRP 0.013 0.002 TRP C 433 HIS 0.006 0.001 HIS F 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.17 (29440) covalent geometry : angle 0.71386 / 0.38 (40043) SS BOND : bond 0.02754 / 0.93 ( 35) SS BOND : angle 1.74492 / 1.04 ( 70) hydrogen bonds : bond 0.04655 / 3.05 ( 956) hydrogen bonds : angle 4.60797 / 3.17 ( 2664) link_BETA1-4 : bond 0.00169 / 0.13 ( 11) link_BETA1-4 : angle 1.40875 / 0.87 ( 33) link_NAG-ASN : bond 0.00347 / 0.18 ( 15) link_NAG-ASN : angle 2.55094 / 1.73 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9390.33 seconds wall clock time: 161 minutes 0.73 seconds (9660.73 seconds total)